- devel - mailman3.cels.anl.gov

Re: [mpich-devel] binding a new MPI type with fortran
by Tatiana V. Martsinkevich 28 Mar '13

28 Mar '13

Thanks for reply. Yes, unfortunately we need fortran interfaces because most of the applications that we use for testing are written in fortran. Will it be enough if I just add a conversion rule to %parmc2f in ./src/binding/f90/buildface? Something like: 'MPI_Pattern' => 'INTEGER(KIND=MPI_ADDRESS_KIND)', 'MPI_Pattern*' => 'INTEGER(KIND=MPI_ADDRESS_KIND)', And for f77 it will be: 'MPI_Pattern' => 'MPI_Fint *' 'MPI_Pattern*' => 'MPI_Fint *' > Also, as a side note, please use "MPIX_" for nonstandard MPI extensions. It makes nonstandard interfaces very obvious to users and will help prevent potential issues with standardization in the future. Duly noted. Tatiana 2013/3/28 Dave Goodell <goodell(a)mcs.anl.gov>: > On Mar 28, 2013, at 2:16 PM CDT, Tatiana V. Martsinkevich <tanya.manekineko(a)gmail.com> wrote: > >> We are implementing some fault tolerance related functionality in >> MPICH-3.0.2. We define a new MPI type in >> ~/mpich-3.0.2/src/include/mpi.h.in as: >> >> typedef void* MPI_Pattern; >> >> then in the same file we define: >> >> int MPI_Pattern_declare(char* name, MPI_Pattern* handler); >> >> However, when I run autogen.sh and fortran binding script executes it >> gives out: >> >> Pattern_declare: No parm type for MPI_Pattern* (MPI_Pattern*) >> Use of uninitialized value $fparm in pattern match (m//) at >> ./buildiface line 1289, <FD> line 1710. > > Do you want Fortran interfaces at this time or would you be just as happy to have C-only bindings right now? The former will require hacking on one or more of the "buildiface" scripts in the "src/binding/LANGUAGE" directories. The latter can be accomplished by moving your prototypes and types near the end of mpi.h.in, near the prototypes for "MPIX_Mutex_unlock" and "PMPIX_Mutex_unlock". > > Also, as a side note, please use "MPIX_" for nonstandard MPI extensions. It makes nonstandard interfaces very obvious to users and will help prevent potential issues with standardization in the future. > > -Dave >

1 0

Re: [mpich-devel] binding a new MPI type with fortran
by Dave Goodell 28 Mar '13

28 Mar '13

On Mar 28, 2013, at 2:16 PM CDT, Tatiana V. Martsinkevich <tanya.manekineko(a)gmail.com> wrote: > We are implementing some fault tolerance related functionality in > MPICH-3.0.2. We define a new MPI type in > ~/mpich-3.0.2/src/include/mpi.h.in as: > > typedef void* MPI_Pattern; > > then in the same file we define: > > int MPI_Pattern_declare(char* name, MPI_Pattern* handler); > > However, when I run autogen.sh and fortran binding script executes it > gives out: > > Pattern_declare: No parm type for MPI_Pattern* (MPI_Pattern*) > Use of uninitialized value $fparm in pattern match (m//) at > ./buildiface line 1289, <FD> line 1710. Do you want Fortran interfaces at this time or would you be just as happy to have C-only bindings right now? The former will require hacking on one or more of the "buildiface" scripts in the "src/binding/LANGUAGE" directories. The latter can be accomplished by moving your prototypes and types near the end of mpi.h.in, near the prototypes for "MPIX_Mutex_unlock" and "PMPIX_Mutex_unlock". Also, as a side note, please use "MPIX_" for nonstandard MPI extensions. It makes nonstandard interfaces very obvious to users and will help prevent potential issues with standardization in the future. -Dave

1 0

binding a new MPI type with fortran
by Tatiana V. Martsinkevich 28 Mar '13

28 Mar '13

Hello, We are implementing some fault tolerance related functionality in MPICH-3.0.2. We define a new MPI type in ~/mpich-3.0.2/src/include/mpi.h.in as: typedef void* MPI_Pattern; then in the same file we define: int MPI_Pattern_declare(char* name, MPI_Pattern* handler); However, when I run autogen.sh and fortran binding script executes it gives out: Pattern_declare: No parm type for MPI_Pattern* (MPI_Pattern*) Use of uninitialized value $fparm in pattern match (m//) at ./buildiface line 1289, <FD> line 1710. As far as I understand it doesn't know what would be a corresponding fortran type for MPI_Pattern (?) so it can't create a fortran interface of the function. I cannot figure out how to resolve this. Any help would be very much appreciated. with best regards, Tatiana

1 0

Re: [mpich-devel] patch for missing declarations in test suite
by Jim Dinan 21 Mar '13

21 Mar '13

Hi Jeff, If you want to come by my office, I can show you how to split up your patch. 12:30-2pm is totally open for me. ~Jim. On 3/21/13 7:22 AM, Jeff Hammond wrote: > Okay, here is a formatted patch file for both the MTestSleep business > and http://trac.mpich.org/projects/mpich/ticket/1798. I don't really > know how to split the two automatically; I created two patches by hand > last night. > > I have committed locally already so if you know the Git-fu I should be > using, please let me know. > > Thanks, > > Jeff > > On Thu, Mar 21, 2013 at 7:11 AM, Jim Dinan <dinan(a)mcs.anl.gov> wrote: >> Hi Jeff, >> >> These are different changes; the earlier patch you submitted was >> primarily fixing header files: >> >> http://git.mpich.org/mpich.git/commitdiff/617927fb?hp=bda59a264d3889c1eb80b… >> >> I'll take a look at the new patch (or Dave is welcome to handle it, if >> he's already started). >> >> Thanks for the patch, >> ~Jim. >> >> On 03/20/2013 08:20 PM, Jeff Hammond wrote: >>> For some reason I do not see these changes. I attached a patch that >>> implements "s/sleep/MTestSleep/g" in case it hasn't been done yet. >>> >>> Jeff >>> >>> On Thu, Feb 21, 2013 at 3:43 PM, Jim Dinan <dinan(a)mcs.anl.gov> wrote: >>>> Hi Jeff, >>>> >>>> Already done, and committed in 617927fb. >>>> >>>> Thanks for the patch, >>>> ~Jim. >>>> >>>> >>>> On 2/21/13 3:35 PM, Jeff Hammond wrote: >>>>> >>>>> I'll see if I can make the patch Windows-safe then and resubmit. >>>>> >>>>> Jeff >>>>> >>>>> On Thu, Feb 21, 2013 at 1:18 PM, William Gropp <wgropp(a)illinois.edu> >>>>> wrote: >>>>>> >>>>>> unistd.h is not part of C - it is for Unix and Unix-like systems. There >>>>>> is >>>>>> a test for this file in configure.ac that should be used, and the Unixism >>>>>> in >>>>>> the test should be removed or protected. The test programs should not >>>>>> assume Unix/POSIX/Linux. The other fixes look good. >>>>>> >>>>>> Bill >>>>>> >>>>>> William Gropp >>>>>> Director, Parallel Computing Institute >>>>>> Deputy Director for Research >>>>>> Institute for Advanced Computing Applications and Technologies >>>>>> Thomas M. Siebel Chair in Computer Science >>>>>> University of Illinois Urbana-Champaign >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On Feb 18, 2013, at 6:47 AM, Jeff Hammond wrote: >>>>>> >>>>>> I'm submitting this via email because Trac is hosed right now (I >>>>>> assume it will be fixed in a few hours, but I don't want to enqueue >>>>>> this in my head that long). >>>>>> >>>>>> LLVM complained about use of undeclared functions being invalid in >>>>>> C99. I fixed them in the attached patch, which is copied below. >>>>>> >>>>>> The fix to test/mpi/rma/mutex_bench.c depends upon the patch to >>>>>> test/mpi/rma/Makefile.am because otherwise the header will not be >>>>>> found. >>>>>> >>>>>> Best, >>>>>> >>>>>> Jeff >>>>>> >>>>>> $ cat test.patch >>>>>> diff --git a/test/mpi/coll/nonblocking3.c b/test/mpi/coll/nonblocking3.c >>>>>> index b1f66dd..8e896b7 100644 >>>>>> --- a/test/mpi/coll/nonblocking3.c >>>>>> +++ b/test/mpi/coll/nonblocking3.c >>>>>> @@ -16,6 +16,7 @@ >>>>>> #include "mpi.h" >>>>>> #include <stdlib.h> >>>>>> #include <stdio.h> >>>>>> +#include <unistd.h> >>>>>> #include <string.h> >>>>>> #include <assert.h> >>>>>> /* USE_STRICT_MPI may be defined in mpitestconf.h */ >>>>>> diff --git a/test/mpi/f90/attr/attrlangc.c >>>>>> b/test/mpi/f90/attr/attrlangc.c >>>>>> index 6920668..2ee4ef5 100644 >>>>>> --- a/test/mpi/f90/attr/attrlangc.c >>>>>> +++ b/test/mpi/f90/attr/attrlangc.c >>>>>> @@ -124,7 +124,7 @@ void cgetsizes_( MPI_Fint *ptrSize, MPI_Fint >>>>>> *intSize, MPI_Fint *aintSize ) >>>>>> } >>>>>> >>>>>> /* >>>>>> ----------------------------------------------------------------------- >>>>>> */ >>>>>> -/* Copy and delete functions attached to keyvals >>>>>> +/* Copy and delete functions attached to keyvals >>>>>> */ >>>>>> /* >>>>>> ----------------------------------------------------------------------- >>>>>> */ >>>>>> static int CMPI1_COPY_FN( MPI_Comm comm, int keyval, void *extra, >>>>>> void *inval, void *outval, int *flag ) >>>>>> diff --git a/test/mpi/manual/mpi_t/nem_fbox_fallback_to_queue_count.c >>>>>> b/test/mpi/manual/mpi_t/nem_fbox_fallback_to_queue_count.c >>>>>> index f045212..9718bbc 100644 >>>>>> --- a/test/mpi/manual/mpi_t/nem_fbox_fallback_to_queue_count.c >>>>>> +++ b/test/mpi/manual/mpi_t/nem_fbox_fallback_to_queue_count.c >>>>>> @@ -17,6 +17,7 @@ >>>>>> #include <stdlib.h> >>>>>> #include <stdint.h> >>>>>> #include <stdio.h> >>>>>> +#include <unistd.h> >>>>>> >>>>>> #define TRY(func) \ >>>>>> do { \ >>>>>> diff --git a/test/mpi/rma/Makefile.am b/test/mpi/rma/Makefile.am >>>>>> index 579721a..76155c5 100644 >>>>>> --- a/test/mpi/rma/Makefile.am >>>>>> +++ b/test/mpi/rma/Makefile.am >>>>>> @@ -155,5 +155,5 @@ get_accumulate_double_derived_SOURCES = >>>>>> get_accumulate.c >>>>>> get_accumulate_int_derived_SOURCES = get_accumulate.c >>>>>> >>>>>> mutex_bench_SOURCES = mutex_bench.c mcs-mutex.c mcs-mutex.h >>>>>> -mutex_bench_shared_CPPFLAGS = -DUSE_WIN_SHARED >>>>>> +mutex_bench_shared_CPPFLAGS = -DUSE_WIN_SHARED $(AM_CPPFLAGS) >>>>>> mutex_bench_shared_SOURCES = mutex_bench.c mcs-mutex.c mcs-mutex.h >>>>>> diff --git a/test/mpi/rma/lockcontention3.c >>>>>> b/test/mpi/rma/lockcontention3.c >>>>>> index 6204e94..196dfb5 100644 >>>>>> --- a/test/mpi/rma/lockcontention3.c >>>>>> +++ b/test/mpi/rma/lockcontention3.c >>>>>> @@ -8,6 +8,7 @@ >>>>>> #include "stdlib.h" >>>>>> #include "mpitest.h" >>>>>> #include <assert.h> >>>>>> +#include <string.h> >>>>>> >>>>>> #define LAST_TEST 14 >>>>>> #define RMA_SIZE 2048 >>>>>> diff --git a/test/mpi/rma/mutex_bench.c b/test/mpi/rma/mutex_bench.c >>>>>> index 098382e..2db24e4 100644 >>>>>> --- a/test/mpi/rma/mutex_bench.c >>>>>> +++ b/test/mpi/rma/mutex_bench.c >>>>>> @@ -12,6 +12,7 @@ >>>>>> #include <assert.h> >>>>>> >>>>>> #include <mpi.h> >>>>>> +#include "mpitest.h" >>>>>> #include "mcs-mutex.h" >>>>>> >>>>>> #define NUM_ITER 1000 >>>>>> >>>>>> -- >>>>>> Jeff Hammond >>>>>> Argonne Leadership Computing Facility >>>>>> University of Chicago Computation Institute >>>>>> jhammond(a)alcf.anl.gov / (630) 252-5381 >>>>>> http://www.linkedin.com/in/jeffhammond >>>>>> https://wiki.alcf.anl.gov/parts/index.php/User:Jhammond >>>>>> <test.patch> >>>>>> >>>>>> >>>>> >>>>> >>>>> >>>> >>> >>> >>> >> > > >

1 0

Re: [mpich-devel] patch for missing declarations in test suite
by Jeff Hammond 21 Mar '13

21 Mar '13

Okay, here is a formatted patch file for both the MTestSleep business and http://trac.mpich.org/projects/mpich/ticket/1798. I don't really know how to split the two automatically; I created two patches by hand last night. I have committed locally already so if you know the Git-fu I should be using, please let me know. Thanks, Jeff On Thu, Mar 21, 2013 at 7:11 AM, Jim Dinan <dinan(a)mcs.anl.gov> wrote: > Hi Jeff, > > These are different changes; the earlier patch you submitted was > primarily fixing header files: > > http://git.mpich.org/mpich.git/commitdiff/617927fb?hp=bda59a264d3889c1eb80b… > > I'll take a look at the new patch (or Dave is welcome to handle it, if > he's already started). > > Thanks for the patch, > ~Jim. > > On 03/20/2013 08:20 PM, Jeff Hammond wrote: >> For some reason I do not see these changes. I attached a patch that >> implements "s/sleep/MTestSleep/g" in case it hasn't been done yet. >> >> Jeff >> >> On Thu, Feb 21, 2013 at 3:43 PM, Jim Dinan <dinan(a)mcs.anl.gov> wrote: >>> Hi Jeff, >>> >>> Already done, and committed in 617927fb. >>> >>> Thanks for the patch, >>> ~Jim. >>> >>> >>> On 2/21/13 3:35 PM, Jeff Hammond wrote: >>>> >>>> I'll see if I can make the patch Windows-safe then and resubmit. >>>> >>>> Jeff >>>> >>>> On Thu, Feb 21, 2013 at 1:18 PM, William Gropp <wgropp(a)illinois.edu> >>>> wrote: >>>>> >>>>> unistd.h is not part of C - it is for Unix and Unix-like systems. There >>>>> is >>>>> a test for this file in configure.ac that should be used, and the Unixism >>>>> in >>>>> the test should be removed or protected. The test programs should not >>>>> assume Unix/POSIX/Linux. The other fixes look good. >>>>> >>>>> Bill >>>>> >>>>> William Gropp >>>>> Director, Parallel Computing Institute >>>>> Deputy Director for Research >>>>> Institute for Advanced Computing Applications and Technologies >>>>> Thomas M. Siebel Chair in Computer Science >>>>> University of Illinois Urbana-Champaign >>>>> >>>>> >>>>> >>>>> >>>>> On Feb 18, 2013, at 6:47 AM, Jeff Hammond wrote: >>>>> >>>>> I'm submitting this via email because Trac is hosed right now (I >>>>> assume it will be fixed in a few hours, but I don't want to enqueue >>>>> this in my head that long). >>>>> >>>>> LLVM complained about use of undeclared functions being invalid in >>>>> C99. I fixed them in the attached patch, which is copied below. >>>>> >>>>> The fix to test/mpi/rma/mutex_bench.c depends upon the patch to >>>>> test/mpi/rma/Makefile.am because otherwise the header will not be >>>>> found. >>>>> >>>>> Best, >>>>> >>>>> Jeff >>>>> >>>>> $ cat test.patch >>>>> diff --git a/test/mpi/coll/nonblocking3.c b/test/mpi/coll/nonblocking3.c >>>>> index b1f66dd..8e896b7 100644 >>>>> --- a/test/mpi/coll/nonblocking3.c >>>>> +++ b/test/mpi/coll/nonblocking3.c >>>>> @@ -16,6 +16,7 @@ >>>>> #include "mpi.h" >>>>> #include <stdlib.h> >>>>> #include <stdio.h> >>>>> +#include <unistd.h> >>>>> #include <string.h> >>>>> #include <assert.h> >>>>> /* USE_STRICT_MPI may be defined in mpitestconf.h */ >>>>> diff --git a/test/mpi/f90/attr/attrlangc.c >>>>> b/test/mpi/f90/attr/attrlangc.c >>>>> index 6920668..2ee4ef5 100644 >>>>> --- a/test/mpi/f90/attr/attrlangc.c >>>>> +++ b/test/mpi/f90/attr/attrlangc.c >>>>> @@ -124,7 +124,7 @@ void cgetsizes_( MPI_Fint *ptrSize, MPI_Fint >>>>> *intSize, MPI_Fint *aintSize ) >>>>> } >>>>> >>>>> /* >>>>> ----------------------------------------------------------------------- >>>>> */ >>>>> -/* Copy and delete functions attached to keyvals >>>>> +/* Copy and delete functions attached to keyvals >>>>> */ >>>>> /* >>>>> ----------------------------------------------------------------------- >>>>> */ >>>>> static int CMPI1_COPY_FN( MPI_Comm comm, int keyval, void *extra, >>>>> void *inval, void *outval, int *flag ) >>>>> diff --git a/test/mpi/manual/mpi_t/nem_fbox_fallback_to_queue_count.c >>>>> b/test/mpi/manual/mpi_t/nem_fbox_fallback_to_queue_count.c >>>>> index f045212..9718bbc 100644 >>>>> --- a/test/mpi/manual/mpi_t/nem_fbox_fallback_to_queue_count.c >>>>> +++ b/test/mpi/manual/mpi_t/nem_fbox_fallback_to_queue_count.c >>>>> @@ -17,6 +17,7 @@ >>>>> #include <stdlib.h> >>>>> #include <stdint.h> >>>>> #include <stdio.h> >>>>> +#include <unistd.h> >>>>> >>>>> #define TRY(func) \ >>>>> do { \ >>>>> diff --git a/test/mpi/rma/Makefile.am b/test/mpi/rma/Makefile.am >>>>> index 579721a..76155c5 100644 >>>>> --- a/test/mpi/rma/Makefile.am >>>>> +++ b/test/mpi/rma/Makefile.am >>>>> @@ -155,5 +155,5 @@ get_accumulate_double_derived_SOURCES = >>>>> get_accumulate.c >>>>> get_accumulate_int_derived_SOURCES = get_accumulate.c >>>>> >>>>> mutex_bench_SOURCES = mutex_bench.c mcs-mutex.c mcs-mutex.h >>>>> -mutex_bench_shared_CPPFLAGS = -DUSE_WIN_SHARED >>>>> +mutex_bench_shared_CPPFLAGS = -DUSE_WIN_SHARED $(AM_CPPFLAGS) >>>>> mutex_bench_shared_SOURCES = mutex_bench.c mcs-mutex.c mcs-mutex.h >>>>> diff --git a/test/mpi/rma/lockcontention3.c >>>>> b/test/mpi/rma/lockcontention3.c >>>>> index 6204e94..196dfb5 100644 >>>>> --- a/test/mpi/rma/lockcontention3.c >>>>> +++ b/test/mpi/rma/lockcontention3.c >>>>> @@ -8,6 +8,7 @@ >>>>> #include "stdlib.h" >>>>> #include "mpitest.h" >>>>> #include <assert.h> >>>>> +#include <string.h> >>>>> >>>>> #define LAST_TEST 14 >>>>> #define RMA_SIZE 2048 >>>>> diff --git a/test/mpi/rma/mutex_bench.c b/test/mpi/rma/mutex_bench.c >>>>> index 098382e..2db24e4 100644 >>>>> --- a/test/mpi/rma/mutex_bench.c >>>>> +++ b/test/mpi/rma/mutex_bench.c >>>>> @@ -12,6 +12,7 @@ >>>>> #include <assert.h> >>>>> >>>>> #include <mpi.h> >>>>> +#include "mpitest.h" >>>>> #include "mcs-mutex.h" >>>>> >>>>> #define NUM_ITER 1000 >>>>> >>>>> -- >>>>> Jeff Hammond >>>>> Argonne Leadership Computing Facility >>>>> University of Chicago Computation Institute >>>>> jhammond(a)alcf.anl.gov / (630) 252-5381 >>>>> http://www.linkedin.com/in/jeffhammond >>>>> https://wiki.alcf.anl.gov/parts/index.php/User:Jhammond >>>>> <test.patch> >>>>> >>>>> >>>> >>>> >>>> >>> >> >> >> > -- Jeff Hammond Argonne Leadership Computing Facility University of Chicago Computation Institute jhammond(a)alcf.anl.gov / (630) 252-5381 http://www.linkedin.com/in/jeffhammond https://wiki.alcf.anl.gov/parts/index.php/User:Jhammond

1 0

Re: [mpich-devel] patch for missing declarations in test suite
by Jim Dinan 21 Mar '13

21 Mar '13

Hi Jeff, These are different changes; the earlier patch you submitted was primarily fixing header files: http://git.mpich.org/mpich.git/commitdiff/617927fb?hp=bda59a264d3889c1eb80b… I'll take a look at the new patch (or Dave is welcome to handle it, if he's already started). Thanks for the patch, ~Jim. On 03/20/2013 08:20 PM, Jeff Hammond wrote: > For some reason I do not see these changes. I attached a patch that > implements "s/sleep/MTestSleep/g" in case it hasn't been done yet. > > Jeff > > On Thu, Feb 21, 2013 at 3:43 PM, Jim Dinan <dinan(a)mcs.anl.gov> wrote: >> Hi Jeff, >> >> Already done, and committed in 617927fb. >> >> Thanks for the patch, >> ~Jim. >> >> >> On 2/21/13 3:35 PM, Jeff Hammond wrote: >>> >>> I'll see if I can make the patch Windows-safe then and resubmit. >>> >>> Jeff >>> >>> On Thu, Feb 21, 2013 at 1:18 PM, William Gropp <wgropp(a)illinois.edu> >>> wrote: >>>> >>>> unistd.h is not part of C - it is for Unix and Unix-like systems. There >>>> is >>>> a test for this file in configure.ac that should be used, and the Unixism >>>> in >>>> the test should be removed or protected. The test programs should not >>>> assume Unix/POSIX/Linux. The other fixes look good. >>>> >>>> Bill >>>> >>>> William Gropp >>>> Director, Parallel Computing Institute >>>> Deputy Director for Research >>>> Institute for Advanced Computing Applications and Technologies >>>> Thomas M. Siebel Chair in Computer Science >>>> University of Illinois Urbana-Champaign >>>> >>>> >>>> >>>> >>>> On Feb 18, 2013, at 6:47 AM, Jeff Hammond wrote: >>>> >>>> I'm submitting this via email because Trac is hosed right now (I >>>> assume it will be fixed in a few hours, but I don't want to enqueue >>>> this in my head that long). >>>> >>>> LLVM complained about use of undeclared functions being invalid in >>>> C99. I fixed them in the attached patch, which is copied below. >>>> >>>> The fix to test/mpi/rma/mutex_bench.c depends upon the patch to >>>> test/mpi/rma/Makefile.am because otherwise the header will not be >>>> found. >>>> >>>> Best, >>>> >>>> Jeff >>>> >>>> $ cat test.patch >>>> diff --git a/test/mpi/coll/nonblocking3.c b/test/mpi/coll/nonblocking3.c >>>> index b1f66dd..8e896b7 100644 >>>> --- a/test/mpi/coll/nonblocking3.c >>>> +++ b/test/mpi/coll/nonblocking3.c >>>> @@ -16,6 +16,7 @@ >>>> #include "mpi.h" >>>> #include <stdlib.h> >>>> #include <stdio.h> >>>> +#include <unistd.h> >>>> #include <string.h> >>>> #include <assert.h> >>>> /* USE_STRICT_MPI may be defined in mpitestconf.h */ >>>> diff --git a/test/mpi/f90/attr/attrlangc.c >>>> b/test/mpi/f90/attr/attrlangc.c >>>> index 6920668..2ee4ef5 100644 >>>> --- a/test/mpi/f90/attr/attrlangc.c >>>> +++ b/test/mpi/f90/attr/attrlangc.c >>>> @@ -124,7 +124,7 @@ void cgetsizes_( MPI_Fint *ptrSize, MPI_Fint >>>> *intSize, MPI_Fint *aintSize ) >>>> } >>>> >>>> /* >>>> ----------------------------------------------------------------------- >>>> */ >>>> -/* Copy and delete functions attached to keyvals >>>> +/* Copy and delete functions attached to keyvals >>>> */ >>>> /* >>>> ----------------------------------------------------------------------- >>>> */ >>>> static int CMPI1_COPY_FN( MPI_Comm comm, int keyval, void *extra, >>>> void *inval, void *outval, int *flag ) >>>> diff --git a/test/mpi/manual/mpi_t/nem_fbox_fallback_to_queue_count.c >>>> b/test/mpi/manual/mpi_t/nem_fbox_fallback_to_queue_count.c >>>> index f045212..9718bbc 100644 >>>> --- a/test/mpi/manual/mpi_t/nem_fbox_fallback_to_queue_count.c >>>> +++ b/test/mpi/manual/mpi_t/nem_fbox_fallback_to_queue_count.c >>>> @@ -17,6 +17,7 @@ >>>> #include <stdlib.h> >>>> #include <stdint.h> >>>> #include <stdio.h> >>>> +#include <unistd.h> >>>> >>>> #define TRY(func) \ >>>> do { \ >>>> diff --git a/test/mpi/rma/Makefile.am b/test/mpi/rma/Makefile.am >>>> index 579721a..76155c5 100644 >>>> --- a/test/mpi/rma/Makefile.am >>>> +++ b/test/mpi/rma/Makefile.am >>>> @@ -155,5 +155,5 @@ get_accumulate_double_derived_SOURCES = >>>> get_accumulate.c >>>> get_accumulate_int_derived_SOURCES = get_accumulate.c >>>> >>>> mutex_bench_SOURCES = mutex_bench.c mcs-mutex.c mcs-mutex.h >>>> -mutex_bench_shared_CPPFLAGS = -DUSE_WIN_SHARED >>>> +mutex_bench_shared_CPPFLAGS = -DUSE_WIN_SHARED $(AM_CPPFLAGS) >>>> mutex_bench_shared_SOURCES = mutex_bench.c mcs-mutex.c mcs-mutex.h >>>> diff --git a/test/mpi/rma/lockcontention3.c >>>> b/test/mpi/rma/lockcontention3.c >>>> index 6204e94..196dfb5 100644 >>>> --- a/test/mpi/rma/lockcontention3.c >>>> +++ b/test/mpi/rma/lockcontention3.c >>>> @@ -8,6 +8,7 @@ >>>> #include "stdlib.h" >>>> #include "mpitest.h" >>>> #include <assert.h> >>>> +#include <string.h> >>>> >>>> #define LAST_TEST 14 >>>> #define RMA_SIZE 2048 >>>> diff --git a/test/mpi/rma/mutex_bench.c b/test/mpi/rma/mutex_bench.c >>>> index 098382e..2db24e4 100644 >>>> --- a/test/mpi/rma/mutex_bench.c >>>> +++ b/test/mpi/rma/mutex_bench.c >>>> @@ -12,6 +12,7 @@ >>>> #include <assert.h> >>>> >>>> #include <mpi.h> >>>> +#include "mpitest.h" >>>> #include "mcs-mutex.h" >>>> >>>> #define NUM_ITER 1000 >>>> >>>> -- >>>> Jeff Hammond >>>> Argonne Leadership Computing Facility >>>> University of Chicago Computation Institute >>>> jhammond(a)alcf.anl.gov / (630) 252-5381 >>>> http://www.linkedin.com/in/jeffhammond >>>> https://wiki.alcf.anl.gov/parts/index.php/User:Jhammond >>>> <test.patch> >>>> >>>> >>> >>> >>> >> > > >

1 0

Re: [mpich-devel] patch for missing declarations in test suite
by Dave Goodell 20 Mar '13

20 Mar '13

Hey Jeff, If you create this (and future) patch(es) with "git format-patch" and attach it (them), you will get proper attribution as the author of the commit in our Git repository. I'm not sure if you care about that, but it also has a few other minor benefits when it comes to accepting your patches. https://www.kernel.org/pub/software/scm/git/docs/git-format-patch.html You'll need to actually commit your change locally before creating the patch this way. If this is confusing or undesirable, let me know and I'll just use the original patch you sent. It's not a big deal either way. -Dave On Mar 20, 2013, at 8:20 PM CDT, Jeff Hammond <jhammond(a)alcf.anl.gov> wrote: > For some reason I do not see these changes. I attached a patch that > implements "s/sleep/MTestSleep/g" in case it hasn't been done yet. > > Jeff > > On Thu, Feb 21, 2013 at 3:43 PM, Jim Dinan <dinan(a)mcs.anl.gov> wrote: >> Hi Jeff, >> >> Already done, and committed in 617927fb. >> >> Thanks for the patch, >> ~Jim. >> >> >> On 2/21/13 3:35 PM, Jeff Hammond wrote: >>> >>> I'll see if I can make the patch Windows-safe then and resubmit. >>> >>> Jeff >>> >>> On Thu, Feb 21, 2013 at 1:18 PM, William Gropp <wgropp(a)illinois.edu> >>> wrote: >>>> >>>> unistd.h is not part of C - it is for Unix and Unix-like systems. There >>>> is >>>> a test for this file in configure.ac that should be used, and the Unixism >>>> in >>>> the test should be removed or protected. The test programs should not >>>> assume Unix/POSIX/Linux. The other fixes look good. >>>> >>>> Bill >>>> >>>> William Gropp >>>> Director, Parallel Computing Institute >>>> Deputy Director for Research >>>> Institute for Advanced Computing Applications and Technologies >>>> Thomas M. Siebel Chair in Computer Science >>>> University of Illinois Urbana-Champaign >>>> >>>> >>>> >>>> >>>> On Feb 18, 2013, at 6:47 AM, Jeff Hammond wrote: >>>> >>>> I'm submitting this via email because Trac is hosed right now (I >>>> assume it will be fixed in a few hours, but I don't want to enqueue >>>> this in my head that long). >>>> >>>> LLVM complained about use of undeclared functions being invalid in >>>> C99. I fixed them in the attached patch, which is copied below. >>>> >>>> The fix to test/mpi/rma/mutex_bench.c depends upon the patch to >>>> test/mpi/rma/Makefile.am because otherwise the header will not be >>>> found. >>>> >>>> Best, >>>> >>>> Jeff >>>> >>>> $ cat test.patch >>>> diff --git a/test/mpi/coll/nonblocking3.c b/test/mpi/coll/nonblocking3.c >>>> index b1f66dd..8e896b7 100644 >>>> --- a/test/mpi/coll/nonblocking3.c >>>> +++ b/test/mpi/coll/nonblocking3.c >>>> @@ -16,6 +16,7 @@ >>>> #include "mpi.h" >>>> #include <stdlib.h> >>>> #include <stdio.h> >>>> +#include <unistd.h> >>>> #include <string.h> >>>> #include <assert.h> >>>> /* USE_STRICT_MPI may be defined in mpitestconf.h */ >>>> diff --git a/test/mpi/f90/attr/attrlangc.c >>>> b/test/mpi/f90/attr/attrlangc.c >>>> index 6920668..2ee4ef5 100644 >>>> --- a/test/mpi/f90/attr/attrlangc.c >>>> +++ b/test/mpi/f90/attr/attrlangc.c >>>> @@ -124,7 +124,7 @@ void cgetsizes_( MPI_Fint *ptrSize, MPI_Fint >>>> *intSize, MPI_Fint *aintSize ) >>>> } >>>> >>>> /* >>>> ----------------------------------------------------------------------- >>>> */ >>>> -/* Copy and delete functions attached to keyvals >>>> +/* Copy and delete functions attached to keyvals >>>> */ >>>> /* >>>> ----------------------------------------------------------------------- >>>> */ >>>> static int CMPI1_COPY_FN( MPI_Comm comm, int keyval, void *extra, >>>> void *inval, void *outval, int *flag ) >>>> diff --git a/test/mpi/manual/mpi_t/nem_fbox_fallback_to_queue_count.c >>>> b/test/mpi/manual/mpi_t/nem_fbox_fallback_to_queue_count.c >>>> index f045212..9718bbc 100644 >>>> --- a/test/mpi/manual/mpi_t/nem_fbox_fallback_to_queue_count.c >>>> +++ b/test/mpi/manual/mpi_t/nem_fbox_fallback_to_queue_count.c >>>> @@ -17,6 +17,7 @@ >>>> #include <stdlib.h> >>>> #include <stdint.h> >>>> #include <stdio.h> >>>> +#include <unistd.h> >>>> >>>> #define TRY(func) \ >>>> do { \ >>>> diff --git a/test/mpi/rma/Makefile.am b/test/mpi/rma/Makefile.am >>>> index 579721a..76155c5 100644 >>>> --- a/test/mpi/rma/Makefile.am >>>> +++ b/test/mpi/rma/Makefile.am >>>> @@ -155,5 +155,5 @@ get_accumulate_double_derived_SOURCES = >>>> get_accumulate.c >>>> get_accumulate_int_derived_SOURCES = get_accumulate.c >>>> >>>> mutex_bench_SOURCES = mutex_bench.c mcs-mutex.c mcs-mutex.h >>>> -mutex_bench_shared_CPPFLAGS = -DUSE_WIN_SHARED >>>> +mutex_bench_shared_CPPFLAGS = -DUSE_WIN_SHARED $(AM_CPPFLAGS) >>>> mutex_bench_shared_SOURCES = mutex_bench.c mcs-mutex.c mcs-mutex.h >>>> diff --git a/test/mpi/rma/lockcontention3.c >>>> b/test/mpi/rma/lockcontention3.c >>>> index 6204e94..196dfb5 100644 >>>> --- a/test/mpi/rma/lockcontention3.c >>>> +++ b/test/mpi/rma/lockcontention3.c >>>> @@ -8,6 +8,7 @@ >>>> #include "stdlib.h" >>>> #include "mpitest.h" >>>> #include <assert.h> >>>> +#include <string.h> >>>> >>>> #define LAST_TEST 14 >>>> #define RMA_SIZE 2048 >>>> diff --git a/test/mpi/rma/mutex_bench.c b/test/mpi/rma/mutex_bench.c >>>> index 098382e..2db24e4 100644 >>>> --- a/test/mpi/rma/mutex_bench.c >>>> +++ b/test/mpi/rma/mutex_bench.c >>>> @@ -12,6 +12,7 @@ >>>> #include <assert.h> >>>> >>>> #include <mpi.h> >>>> +#include "mpitest.h" >>>> #include "mcs-mutex.h" >>>> >>>> #define NUM_ITER 1000 >>>> >>>> -- >>>> Jeff Hammond >>>> Argonne Leadership Computing Facility >>>> University of Chicago Computation Institute >>>> jhammond(a)alcf.anl.gov / (630) 252-5381 >>>> http://www.linkedin.com/in/jeffhammond >>>> https://wiki.alcf.anl.gov/parts/index.php/User:Jhammond >>>> <test.patch> >>>> >>>> >>> >>> >>> >> > > > > -- > Jeff Hammond > Argonne Leadership Computing Facility > University of Chicago Computation Institute > jhammond(a)alcf.anl.gov / (630) 252-5381 > http://www.linkedin.com/in/jeffhammond > https://wiki.alcf.anl.gov/parts/index.php/User:Jhammond > <sleep.patch>

1 0

Re: [mpich-devel] patch for missing declarations in test suite
by Jeff Hammond 20 Mar '13

20 Mar '13

For some reason I do not see these changes. I attached a patch that implements "s/sleep/MTestSleep/g" in case it hasn't been done yet. Jeff On Thu, Feb 21, 2013 at 3:43 PM, Jim Dinan <dinan(a)mcs.anl.gov> wrote: > Hi Jeff, > > Already done, and committed in 617927fb. > > Thanks for the patch, > ~Jim. > > > On 2/21/13 3:35 PM, Jeff Hammond wrote: >> >> I'll see if I can make the patch Windows-safe then and resubmit. >> >> Jeff >> >> On Thu, Feb 21, 2013 at 1:18 PM, William Gropp <wgropp(a)illinois.edu> >> wrote: >>> >>> unistd.h is not part of C - it is for Unix and Unix-like systems. There >>> is >>> a test for this file in configure.ac that should be used, and the Unixism >>> in >>> the test should be removed or protected. The test programs should not >>> assume Unix/POSIX/Linux. The other fixes look good. >>> >>> Bill >>> >>> William Gropp >>> Director, Parallel Computing Institute >>> Deputy Director for Research >>> Institute for Advanced Computing Applications and Technologies >>> Thomas M. Siebel Chair in Computer Science >>> University of Illinois Urbana-Champaign >>> >>> >>> >>> >>> On Feb 18, 2013, at 6:47 AM, Jeff Hammond wrote: >>> >>> I'm submitting this via email because Trac is hosed right now (I >>> assume it will be fixed in a few hours, but I don't want to enqueue >>> this in my head that long). >>> >>> LLVM complained about use of undeclared functions being invalid in >>> C99. I fixed them in the attached patch, which is copied below. >>> >>> The fix to test/mpi/rma/mutex_bench.c depends upon the patch to >>> test/mpi/rma/Makefile.am because otherwise the header will not be >>> found. >>> >>> Best, >>> >>> Jeff >>> >>> $ cat test.patch >>> diff --git a/test/mpi/coll/nonblocking3.c b/test/mpi/coll/nonblocking3.c >>> index b1f66dd..8e896b7 100644 >>> --- a/test/mpi/coll/nonblocking3.c >>> +++ b/test/mpi/coll/nonblocking3.c >>> @@ -16,6 +16,7 @@ >>> #include "mpi.h" >>> #include <stdlib.h> >>> #include <stdio.h> >>> +#include <unistd.h> >>> #include <string.h> >>> #include <assert.h> >>> /* USE_STRICT_MPI may be defined in mpitestconf.h */ >>> diff --git a/test/mpi/f90/attr/attrlangc.c >>> b/test/mpi/f90/attr/attrlangc.c >>> index 6920668..2ee4ef5 100644 >>> --- a/test/mpi/f90/attr/attrlangc.c >>> +++ b/test/mpi/f90/attr/attrlangc.c >>> @@ -124,7 +124,7 @@ void cgetsizes_( MPI_Fint *ptrSize, MPI_Fint >>> *intSize, MPI_Fint *aintSize ) >>> } >>> >>> /* >>> ----------------------------------------------------------------------- >>> */ >>> -/* Copy and delete functions attached to keyvals >>> +/* Copy and delete functions attached to keyvals >>> */ >>> /* >>> ----------------------------------------------------------------------- >>> */ >>> static int CMPI1_COPY_FN( MPI_Comm comm, int keyval, void *extra, >>> void *inval, void *outval, int *flag ) >>> diff --git a/test/mpi/manual/mpi_t/nem_fbox_fallback_to_queue_count.c >>> b/test/mpi/manual/mpi_t/nem_fbox_fallback_to_queue_count.c >>> index f045212..9718bbc 100644 >>> --- a/test/mpi/manual/mpi_t/nem_fbox_fallback_to_queue_count.c >>> +++ b/test/mpi/manual/mpi_t/nem_fbox_fallback_to_queue_count.c >>> @@ -17,6 +17,7 @@ >>> #include <stdlib.h> >>> #include <stdint.h> >>> #include <stdio.h> >>> +#include <unistd.h> >>> >>> #define TRY(func) \ >>> do { \ >>> diff --git a/test/mpi/rma/Makefile.am b/test/mpi/rma/Makefile.am >>> index 579721a..76155c5 100644 >>> --- a/test/mpi/rma/Makefile.am >>> +++ b/test/mpi/rma/Makefile.am >>> @@ -155,5 +155,5 @@ get_accumulate_double_derived_SOURCES = >>> get_accumulate.c >>> get_accumulate_int_derived_SOURCES = get_accumulate.c >>> >>> mutex_bench_SOURCES = mutex_bench.c mcs-mutex.c mcs-mutex.h >>> -mutex_bench_shared_CPPFLAGS = -DUSE_WIN_SHARED >>> +mutex_bench_shared_CPPFLAGS = -DUSE_WIN_SHARED $(AM_CPPFLAGS) >>> mutex_bench_shared_SOURCES = mutex_bench.c mcs-mutex.c mcs-mutex.h >>> diff --git a/test/mpi/rma/lockcontention3.c >>> b/test/mpi/rma/lockcontention3.c >>> index 6204e94..196dfb5 100644 >>> --- a/test/mpi/rma/lockcontention3.c >>> +++ b/test/mpi/rma/lockcontention3.c >>> @@ -8,6 +8,7 @@ >>> #include "stdlib.h" >>> #include "mpitest.h" >>> #include <assert.h> >>> +#include <string.h> >>> >>> #define LAST_TEST 14 >>> #define RMA_SIZE 2048 >>> diff --git a/test/mpi/rma/mutex_bench.c b/test/mpi/rma/mutex_bench.c >>> index 098382e..2db24e4 100644 >>> --- a/test/mpi/rma/mutex_bench.c >>> +++ b/test/mpi/rma/mutex_bench.c >>> @@ -12,6 +12,7 @@ >>> #include <assert.h> >>> >>> #include <mpi.h> >>> +#include "mpitest.h" >>> #include "mcs-mutex.h" >>> >>> #define NUM_ITER 1000 >>> >>> -- >>> Jeff Hammond >>> Argonne Leadership Computing Facility >>> University of Chicago Computation Institute >>> jhammond(a)alcf.anl.gov / (630) 252-5381 >>> http://www.linkedin.com/in/jeffhammond >>> https://wiki.alcf.anl.gov/parts/index.php/User:Jhammond >>> <test.patch> >>> >>> >> >> >> > -- Jeff Hammond Argonne Leadership Computing Facility University of Chicago Computation Institute jhammond(a)alcf.anl.gov / (630) 252-5381 http://www.linkedin.com/in/jeffhammond https://wiki.alcf.anl.gov/parts/index.php/User:Jhammond

1 0

Re: [mpich-devel] memory profiling HOWTO?
by Jeff Hammond 23 Feb '13

23 Feb '13

I think I need to override MPIU_Malloc myself for this but I will also try --enable-g=mem and MPIU_trspace to see how the information I get from that lines up with what I get from the BGQ SPI (which can track everything: heap, stack, shm, ...). Thanks for all the pointers. Jeff On Sat, Feb 23, 2013 at 10:16 AM, Dave Goodell <goodell(a)mcs.anl.gov> wrote: > There are two kinds of memory that MPICH with ch3:nemesis allocates: > > 1) regular heap memory via malloc (with interposition possible via MPIU_Malloc and friends) > > 2) shared memory via one of the usual mechanisms (mmap, shm_open, etc.) > > You can determine the current amount of #1 by calling "MPIU_trspace" as long as you configure with "--enable-g=mem" (or some superset thereof). You'll get some additional performance overhead when allocating/freeing memory if you configure this way, since MPICH is doing some additional allocation and bookkeeping in order to track this information for you. If you need a lower overhead method for doing this, you'll need to modify/intercept MPIU_Malloc and friends yourself. You'll need an "extern" declaration for "MPIU_trspace" in order to call it from your test program. > > You can use the attached (untested against HEAD) patch to give you a hook for #2. You'll need to throw down an "extern" declaration for the routine in your test program as well. > > -Dave > > > > > On Feb 22, 2013, at 9:28 AM CST, Jim Dinan wrote: > >> Jeff, >> >> Which memory are you interested in -- memory the application allocates, or memory that MPICH allocates? If the former, you can use the PMPI interface to hook MPI_Alloc/Free_mem. If you are interested in MPICH internal memory use, Dave can probably give the most informed answer. I would probably just modify MPIU_Malloc. >> >> ~Jim. >> >> On 2/22/13 8:44 AM, Jeff Hammond wrote: >>> Is there any documentation of how to properly instrument MPICH with >>> memory profiling? I understand MPIU_MALLOC allows me to do this. >>> >>> My goal is to merely print out every time memory is allocated larger >>> than a particular size. I'd also like the rank to show up in the >>> output. >>> >>> Please RTM me if the M exists. Source comments are also a good M if >>> they are correct and sufficiently complete. >>> >>> Thanks! >>> >>> Jeff >>> > > -- Jeff Hammond Argonne Leadership Computing Facility University of Chicago Computation Institute jhammond(a)alcf.anl.gov / (630) 252-5381 http://www.linkedin.com/in/jeffhammond https://wiki.alcf.anl.gov/parts/index.php/User:Jhammond

1 0

Re: [mpich-devel] memory profiling HOWTO?
by Jeff Hammond 23 Feb '13

23 Feb '13

I'm interested in MPICH internal allocation. I'm trying to figure out all the places in BGQ-MPI where O(p) memory is required. Jeff On Fri, Feb 22, 2013 at 9:28 AM, Jim Dinan <dinan(a)mcs.anl.gov> wrote: > Jeff, > > Which memory are you interested in -- memory the application allocates, or > memory that MPICH allocates? If the former, you can use the PMPI interface > to hook MPI_Alloc/Free_mem. If you are interested in MPICH internal memory > use, Dave can probably give the most informed answer. I would probably just > modify MPIU_Malloc. > > ~Jim. > > > On 2/22/13 8:44 AM, Jeff Hammond wrote: >> >> Is there any documentation of how to properly instrument MPICH with >> memory profiling? I understand MPIU_MALLOC allows me to do this. >> >> My goal is to merely print out every time memory is allocated larger >> than a particular size. I'd also like the rank to show up in the >> output. >> >> Please RTM me if the M exists. Source comments are also a good M if >> they are correct and sufficiently complete. >> >> Thanks! >> >> Jeff >> > -- Jeff Hammond Argonne Leadership Computing Facility University of Chicago Computation Institute jhammond(a)alcf.anl.gov / (630) 252-5381 http://www.linkedin.com/in/jeffhammond https://wiki.alcf.anl.gov/parts/index.php/User:Jhammond

1 0