Fenix new #225

rfvander · 2017-07-25T17:03:21Z

Fenix_new adds Fenix versions of Stencil, Transpose, AMR, and Sparse to the repo, using split main programs to make sure the compiler can optimize the performance sensitive part of the kernels. The implementations have been tested with OpenMPIv17.1

… required making certain functions in header files static to avoid duplicates.

…econstructing kernel data structures (especially sparse matrix elements) after a fault.

…lytical data recovery.

…x.in to make sure ULFM sees the whole path to mpirun

…cation in Fenix build tree

jeffhammond · 2017-07-25T17:34:01Z

It is not important but OpenMPIv17.1 doesn't exist. Do you mean Open-MPI 1.7.1?

It sounds like I need to add Open-MPI to Travis.

rfvander · 2017-07-25T17:39:00Z

Apologies. Indeed, OpenMPI 1.7.1 is the version required at present. It is obtained using Mercurial. I will send instructions. The Fenix library is also required. I will send instructions for that as well.

jeffhammond · 2017-07-27T17:36:23Z

Please fix issues with time_step/timestep.o. Thanks.

/home/travis/build/ParRes/Kernels/PRK-deps/bin/mpicc -std=c99 -O3 -DMPI -DRESTRICT_KEYWORD=0 -DVERBOSE=0  -DDOUBLE=1   -DRADIUS=2  -DSTAR=1 -DLOOPGEN=0   -I../../include -c amr.c
amr.c: In function ‘main’:
amr.c:475:75: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=]
       printf("ERROR: rank %d's BG work tile smaller than stencil radius: %d\n",
                                                                           ^
amr.c:700:75: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘long int’ [-Wformat=]
       printf("ERROR: rank %d's work tile %d smaller than stencil radius: %d\n",
                                                                           ^
amr.c:815:6: warning: implicit declaration of function ‘time_step’ [-Wimplicit-function-declaration]
      time_step(Num_procs, Num_procs_bg, Num_procs_bgx, Num_procs_bgy,
      ^~~~~~~~~
/home/travis/build/ParRes/Kernels/PRK-deps/bin/mpicc -std=c99 -O3 -DMPI -DRESTRICT_KEYWORD=0 -DVERBOSE=0  -DDOUBLE=1   -DRADIUS=2  -DSTAR=1 -DLOOPGEN=0   -I../../include -c ../../common/MPI_bail_out.c
/home/travis/build/ParRes/Kernels/PRK-deps/bin/mpicc -std=c99 -O3 -DMPI -DRESTRICT_KEYWORD=0 -DVERBOSE=0  -DDOUBLE=1   -DRADIUS=2  -DSTAR=1 -DLOOPGEN=0   -I../../include -c ../../common/wtime.c
make[1]: *** No rule to make target `timestep.c', needed by `timestep.o'.  Stop.
make[1]: Leaving directory `/home/travis/build/ParRes/Kernels/MPI1/AMR'
make: *** [allmpi1] Error 2

rfvander · 2017-07-27T17:39:28Z

Thanks for getting cracking on my pull request. I'll figure out what went wrong and fix it.

rfvander · 2017-07-27T17:45:41Z

Can you check to see if there is a conflict in make.common? I have this in the version that should have been committed and push to branch Fenix_new:

...
timestep.o: timestep.c
        $(CCOMPILER) $(CFLAGS) $(TUNEFLAGS) $(INCLUDEPATHSPLUS) -c $<
 
wtime.o:$(COMMON)/wtime.c
        $(CCOMPILER) $(CFLAGS) $(TUNEFLAGS) $(INCLUDEPATHSPLUS) -c $<
 
random_draw.o:$(COMMON)/random_draw.c
        $(CCOMPILER) $(CFLAGS) $(TUNEFLAGS) $(INCLUDEPATHSPLUS) -c $<
 
MPI_bail_out.o:$(COMMON)/MPI_bail_out.c
        $(CCOMPILER) $(CFLAGS) $(TUNEFLAGS) $(INCLUDEPATHSPLUS) -c $<
...

jeffhammond · 2017-07-27T17:57:00Z

Just push to your branch and GitHub will determine if there is a conflict.

rfvander · 2017-07-27T18:01:21Z

That was a typo on my part. I had already pushed my branch.

…ed codes will differ from one system to the next.

jeffhammond · 2017-08-17T22:49:12Z

@rfvander The problem is that timestep.c lives in PRK/FENIX/AMR/ not PRK/MPI1/AMR/. Also, it depends on fenix.h.

You need to implement MPI1's AMR without Fenix-related dependencies.

jrhammon-mac01:AMR jrhammon$ make amr
mpicc -std=c99 -g -O3 -mtune=native -ffast-math -DMPI -DRESTRICT_KEYWORD=0 -DVERBOSE=0  -DDOUBLE=1   -DRADIUS=2  -DSTAR=1 -DLOOPGEN=0   -I../../include -c timestep.c
In file included from timestep.c(34):
../../include/par-res-kern_fenix.h(34): catastrophic error: cannot open source file "fenix.h"
  #include <fenix.h>

jeffhammond · 2017-08-17T22:51:20Z

Fixed in fa2ce89

rfvander · 2017-08-17T23:00:12Z

I'm not sure I understand. I had pulled the body out of the main iteration loop only for the Fenix implementations of the PRKs, and in that case Fenix-related dependencies would always be resolved. I had not done this for MPI1, so there should not be a problem.
Of course, if you want to reuse that timestep.c file for MPI1, which is legit, we should make sure there are no Fenix dependencies. None is needed for timestep.c, because no Fenix calls are made inside. If I put fenix.h in timestep.c, it can be removed.

jeffhammond · 2017-08-17T23:20:59Z

Try to build allmpi1 without the change in my patch. I don't see how it can succeed.

jeffhammond · 2017-08-17T23:21:31Z

MPI1/AMR/amr.c separated time_step into a separate function as well...

rfvander · 2017-08-17T23:29:07Z

That is actually a matter of garbage collection. File timestep.c in that directory is not used to build the kernel. It must be left over from my work on Fenix, and should be removed.

[rfvander@esgmonster esg-prk-devel]$ make allmpi1 PRK_FLAGS=-std:c99
cd MPI1/Synch_global;        make global    "DEFAULT_OPT_FLAGS   = -std:c99"
make[1]: Entering directory `/home/rfvander/esg-prk-devel/MPI1/Synch_global'
mpiicc -std:c99 -DMPI -DVERBOSE=0    -I../../include -c global.c
mpiicc -std:c99 -DMPI -DVERBOSE=0    -I../../include -c ../../common/MPI_bail_out.c
mpiicc -std:c99 -DMPI -DVERBOSE=0    -I../../include -c ../../common/wtime.c
mpiicc -o global   -std:c99 -DMPI global.o MPI_bail_out.o wtime.o  
make[1]: Leaving directory `/home/rfvander/esg-prk-devel/MPI1/Synch_global'
cd MPI1/Synch_p2p;           make p2p       "DEFAULT_OPT_FLAGS   = -std:c99"
make[1]: Entering directory `/home/rfvander/esg-prk-devel/MPI1/Synch_p2p'
mpiicc -std:c99 -DMPI -DVERBOSE=0  -DRESTRICT_KEYWORD=0  -I../../include -c p2p.c
mpiicc -std:c99 -DMPI -DVERBOSE=0  -DRESTRICT_KEYWORD=0  -I../../include -c ../../common/MPI_bail_out.c
mpiicc -std:c99 -DMPI -DVERBOSE=0  -DRESTRICT_KEYWORD=0  -I../../include -c ../../common/wtime.c
mpiicc -o p2p   -std:c99 -DMPI p2p.o MPI_bail_out.o wtime.o  
make[1]: Leaving directory `/home/rfvander/esg-prk-devel/MPI1/Synch_p2p'
cd MPI1/Sparse;              make sparse    "DEFAULT_OPT_FLAGS   = -std:c99"
make[1]: Entering directory `/home/rfvander/esg-prk-devel/MPI1/Sparse'
mpiicc -std:c99  -DMPI -DVERBOSE=0  -DSCRAMBLE=1 -DTESTDENSE=0 -DRESTRICT_KEYWORD=0  -I../../include -c sparse.c
mpiicc -std:c99  -DMPI -DVERBOSE=0  -DSCRAMBLE=1 -DTESTDENSE=0 -DRESTRICT_KEYWORD=0  -I../../include -c ../../common/MPI_bail_out.c
mpiicc -std:c99  -DMPI -DVERBOSE=0  -DSCRAMBLE=1 -DTESTDENSE=0 -DRESTRICT_KEYWORD=0  -I../../include -c ../../common/wtime.c
mpiicc -o sparse   -std:c99  -DMPI sparse.o MPI_bail_out.o wtime.o  
make[1]: Leaving directory `/home/rfvander/esg-prk-devel/MPI1/Sparse'
cd MPI1/Transpose;           make transpose "DEFAULT_OPT_FLAGS   = -std:c99"
make[1]: Entering directory `/home/rfvander/esg-prk-devel/MPI1/Transpose'
mpiicc -std:c99 -std=c99 -DMPI -DVERBOSE=0  -DRESTRICT_KEYWORD=0 -DSYNCHRONOUS=0  -I../../include -c transpose.c
mpiicc -std:c99 -std=c99 -DMPI -DVERBOSE=0  -DRESTRICT_KEYWORD=0 -DSYNCHRONOUS=0  -I../../include -c ../../common/MPI_bail_out.c
mpiicc -std:c99 -std=c99 -DMPI -DVERBOSE=0  -DRESTRICT_KEYWORD=0 -DSYNCHRONOUS=0  -I../../include -c ../../common/wtime.c
mpiicc -o transpose   -std:c99 -std=c99 -DMPI transpose.o MPI_bail_out.o wtime.o  
make[1]: Leaving directory `/home/rfvander/esg-prk-devel/MPI1/Transpose'
cd MPI1/Stencil;             make stencil   "DEFAULT_OPT_FLAGS   = -std:c99"
make[1]: Entering directory `/home/rfvander/esg-prk-devel/MPI1/Stencil'
mpiicc -std:c99 -DMPI -DRESTRICT_KEYWORD=0 -DVERBOSE=0 -DLOOPGEN=0 -DDOUBLE=1   -DRADIUS=2 -DSTAR=1   -I../../include -c stencil.c
mpiicc -std:c99 -DMPI -DRESTRICT_KEYWORD=0 -DVERBOSE=0 -DLOOPGEN=0 -DDOUBLE=1   -DRADIUS=2 -DSTAR=1   -I../../include -c ../../common/MPI_bail_out.c
mpiicc -std:c99 -DMPI -DRESTRICT_KEYWORD=0 -DVERBOSE=0 -DLOOPGEN=0 -DDOUBLE=1   -DRADIUS=2 -DSTAR=1   -I../../include -c ../../common/wtime.c
mpiicc -o stencil   -std:c99 -DMPI stencil.o MPI_bail_out.o wtime.o  -lm
make[1]: Leaving directory `/home/rfvander/esg-prk-devel/MPI1/Stencil'
cd MPI1/DGEMM;               make dgemm     "DEFAULT_OPT_FLAGS   = -std:c99"
make[1]: Entering directory `/home/rfvander/esg-prk-devel/MPI1/DGEMM'
mpiicc -std:c99  -DMPI -DBOFFSET=12 -DVERBOSE=0   -I../../include -c dgemm.c
mpiicc -std:c99  -DMPI -DBOFFSET=12 -DVERBOSE=0   -I../../include -c ../../common/MPI_bail_out.c
mpiicc -std:c99  -DMPI -DBOFFSET=12 -DVERBOSE=0   -I../../include -c ../../common/wtime.c
mpiicc -o dgemm   -std:c99  -DMPI dgemm.o MPI_bail_out.o wtime.o   -lm
make[1]: Leaving directory `/home/rfvander/esg-prk-devel/MPI1/DGEMM'
cd MPI1/Nstream;             make nstream   "DEFAULT_OPT_FLAGS   = -std:c99"
make[1]: Entering directory `/home/rfvander/esg-prk-devel/MPI1/Nstream'
mpiicc -std:c99 -DMPI -DVERBOSE=0   -DRESTRICT_KEYWORD=0  -I../../include -c nstream.c
mpiicc -std:c99 -DMPI -DVERBOSE=0   -DRESTRICT_KEYWORD=0  -I../../include -c ../../common/MPI_bail_out.c
mpiicc -std:c99 -DMPI -DVERBOSE=0   -DRESTRICT_KEYWORD=0  -I../../include -c ../../common/wtime.c
mpiicc -o nstream   -std:c99 -DMPI nstream.o MPI_bail_out.o wtime.o  
make[1]: Leaving directory `/home/rfvander/esg-prk-devel/MPI1/Nstream'
cd MPI1/Reduce;              make reduce    "DEFAULT_OPT_FLAGS   = -std:c99"
make[1]: Entering directory `/home/rfvander/esg-prk-devel/MPI1/Reduce'
mpiicc -std:c99 -DMPI -DVERBOSE=0  -DRESTRICT_KEYWORD=0  -I../../include -c reduce.c
mpiicc -std:c99 -DMPI -DVERBOSE=0  -DRESTRICT_KEYWORD=0  -I../../include -c ../../common/MPI_bail_out.c
mpiicc -std:c99 -DMPI -DVERBOSE=0  -DRESTRICT_KEYWORD=0  -I../../include -c ../../common/wtime.c
mpiicc -o reduce   -std:c99 -DMPI reduce.o MPI_bail_out.o wtime.o  
make[1]: Leaving directory `/home/rfvander/esg-prk-devel/MPI1/Reduce'
cd MPI1/Random;              make random    "DEFAULT_OPT_FLAGS   = -std:c99"
make[1]: Entering directory `/home/rfvander/esg-prk-devel/MPI1/Random'
mpiicc -std:c99 -DMPI -DRESTRICT_KEYWORD=0 -DLONG_IS_64BITS=0 -DVERBOSE=0      -DLOOKAHEAD=1024  -I../../include -c random.c
mpiicc -std:c99 -DMPI -DRESTRICT_KEYWORD=0 -DLONG_IS_64BITS=0 -DVERBOSE=0      -DLOOKAHEAD=1024  -I../../include -c ../../common/MPI_bail_out.c
mpiicc -std:c99 -DMPI -DRESTRICT_KEYWORD=0 -DLONG_IS_64BITS=0 -DVERBOSE=0      -DLOOKAHEAD=1024  -I../../include -c ../../common/wtime.c
mpiicc -o random   -std:c99 -DMPI random.o MPI_bail_out.o wtime.o  
make[1]: Leaving directory `/home/rfvander/esg-prk-devel/MPI1/Random'
cd MPI1/Branch;              make branch    "DEFAULT_OPT_FLAGS   = -std:c99"  \
                                                       "MATRIX_RANK         = 5"        \
                                                       "NUMBER_OF_FUNCTIONS = 40"
make[1]: Entering directory `/home/rfvander/esg-prk-devel/MPI1/Branch'
mpiicc -std:c99  -DMPI -DRESTRICT_KEYWORD=0 -DVERBOSE=0   -I../../include -c branch.c
mpiicc -std:c99  -DMPI -DRESTRICT_KEYWORD=0 -DVERBOSE=0   -I../../include -c ../../common/MPI_bail_out.c
mpiicc -std:c99  -DMPI -DRESTRICT_KEYWORD=0 -DVERBOSE=0   -I../../include -c ../../common/wtime.c
mpiicc -std:c99  -DMPI -DRESTRICT_KEYWORD=0 -DVERBOSE=0   -I../../include -c func.c
mpiicc -o branch   -std:c99  -DMPI branch.o MPI_bail_out.o wtime.o func.o  
make[1]: Leaving directory `/home/rfvander/esg-prk-devel/MPI1/Branch'
cd MPI1/PIC-static;          make pic       "DEFAULT_OPT_FLAGS   = -std:c99"
make[1]: Entering directory `/home/rfvander/esg-prk-devel/MPI1/PIC-static'
mpiicc -std:c99  -DMPI -DVERBOSE=0   -DRESTRICT_KEYWORD=0  -I../../include -c pic.c
mpiicc -std:c99  -DMPI -DVERBOSE=0   -DRESTRICT_KEYWORD=0  -I../../include -c ../../common/MPI_bail_out.c
mpiicc -std:c99  -DMPI -DVERBOSE=0   -DRESTRICT_KEYWORD=0  -I../../include -c ../../common/wtime.c
mpiicc -std:c99  -DMPI -DVERBOSE=0   -DRESTRICT_KEYWORD=0  -I../../include -c ../../common/random_draw.c
mpiicc -o pic   -std:c99  -DMPI pic.o MPI_bail_out.o wtime.o random_draw.o  -lm
make[1]: Leaving directory `/home/rfvander/esg-prk-devel/MPI1/PIC-static'
cd MPI1/AMR;                 make amr       "DEFAULT_OPT_FLAGS   = -std:c99"
make[1]: Entering directory `/home/rfvander/esg-prk-devel/MPI1/AMR'
mpiicc -std:c99 -DMPI -DRESTRICT_KEYWORD=0 -DVERBOSE=0  -DDOUBLE=1   -DRADIUS=2  -DSTAR=1 -DLOOPGEN=0   -I../../include -c amr.c
mpiicc -std:c99 -DMPI -DRESTRICT_KEYWORD=0 -DVERBOSE=0  -DDOUBLE=1   -DRADIUS=2  -DSTAR=1 -DLOOPGEN=0   -I../../include -c ../../common/MPI_bail_out.c
mpiicc -std:c99 -DMPI -DRESTRICT_KEYWORD=0 -DVERBOSE=0  -DDOUBLE=1   -DRADIUS=2  -DSTAR=1 -DLOOPGEN=0   -I../../include -c ../../common/wtime.c
mpiicc -o amr   -std:c99 -DMPI amr.o MPI_bail_out.o wtime.o  -lm
make[1]: Leaving directory `/home/rfvander/esg-prk-devel/MPI1/AMR'
[rfvander@esgmonster esg-prk-devel]$

jeffhammond · 2017-08-17T23:35:00Z

Then where does https://github.com/ParRes/Kernels/blob/Fenix_new/MPI1/AMR/amr.c#L815 come from?

jeffhammond · 2017-08-17T23:37:53Z

049f59a is when the definition of time_step was removed from that file...

commit 049f59ab89c7ea4d7530d80a1b3729cfc558736a
Author: rfvander <[email protected]>
Date:   Fri Jun 9 17:10:52 2017 -0700

    Making structure of MPI1 and FENIX version of AMR identical. This alo required making certain functions in header files static to avoid duplicates.

rfvander · 2017-08-17T23:37:59Z

Ah, I was on branch master. I will check this out later tonight. Sorry.

jeffhammond · 2017-08-18T05:26:38Z

It builds clean now but time_step declaration didn't match definition when I tried to fix it. Since it has 4700 arguments, I'll let you handle that issue.

rfvander · 2017-08-18T05:46:01Z

OK, I'll take care of it. The reason MPI1/AMR has the split structure is because I wanted to create a simple example for the Fenix version. I should have reverted to the original form, but somehow managed to delete it. But we could have a longer discussion about the desirability of the split. I purposely tried to keep the kernels flat (a single file and, if possible, a single function, except library calls), so that the compiler always has maximum knowledge without the user having to use compiler-specific flags to enable cross function and cross module optimization.
This worked fine when the kernels were very simple. But AMR and PIC stretched that and couldn't reasonably be implemented as one function. So I introduced a few functions (smallest possible).
Then Fenix came along, which was actually hurt by a flat file/single function. setjmp (in macro Fenix_Init) disables compiler optimizations within its lexical scope, so it had to be isolated. Most logical was to extract the portion that was time-critical, namely the time step.
We could decide to isolate the time step in all kernels (this would be quite a lot). I prefer consistency, so all or nothing. Simplest at present is to let MPI1/AMR revert to the original structure for now, and only do the split for Fenix, where we have an overriding reason to do it.

the merge fix in amr.c was trivial but the new code is not used so i don't really know what is going on with it.

rfvander added 9 commits June 9, 2017 17:10

Making structure of MPI1 and FENIX version of AMR identical. This alo…

049f59a

… required making certain functions in header files static to avoid duplicates.

Adding Fenix implementation of Sparse (SpMV).

72399af

Adding a comment to README explaining larger than usual overhead of r…

20abfba

…econstructing kernel data structures (especially sparse matrix elements) after a fault.

Correcting comments about value of iter_init for recovered ranks.

978ae6a

Remove Fenix version of sparse; too complicated to implement with ana…

427eb03

…lytical data recovery.

cleaning up FENIX directories via global Makefile, and fixing runfeni…

ded8b8f

…x.in to make sure ULFM sees the whole path to mpirun

modifying FENIX Makefiles to account for move of fenix.h to proper lo…

8380b02

…cation in Fenix build tree

make.defs should not be in repo.

6e7be72

Merge branch 'master' into Fenix_new

78c0b0f

rfvander requested a review from jeffhammond July 25, 2017 17:04

rfvander assigned jeffhammond Jul 25, 2017

jeffhammond added the MPI label Jul 25, 2017

rfvander and others added 2 commits August 4, 2017 11:25

Adding ULFMRUNFLAG to environment, because the way to run Fenix-enabl…

5058e9c

…ed codes will differ from one system to the next.

Merge branch 'master' into Fenix_new

8b9eec0

fix build issue

fa2ce89

jeffhammond and others added 2 commits September 7, 2017 14:36

Merge branch 'master' into Fenix_new

d8eade1

Merge branch 'master' into Fenix_new

5955b3d

the merge fix in amr.c was trivial but the new code is not used so i don't really know what is going on with it.

jeffhammond changed the base branch from master to default June 16, 2020 15:53

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Fenix new #225

Fenix new #225

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Fenix new #225

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