[petsc-users] Confusion/failures about the tests involved in including Hypre
Daniel Stone
daniel.stone at opengosim.com
Thu Jul 20 04:10:26 CDT 2023
Hi All,
Many thanks for the detailed explainations and ideas!
I tried skipping the test. When it came time to do the build itself (make
$PETSC_DIR... all) I get some failures, unsurprisingly:
--------------------------------
FC arch-mswin-c-opt/obj/dm/f90-mod/petscdmplexmod.o
CC arch-mswin-c-opt/obj/ksp/pc/impls/hypre/ftn-custom/zhypref.o
CC arch-mswin-c-opt/obj/ksp/pc/impls/hypre/ftn-auto/hypref.o
CC arch-mswin-c-opt/obj/ksp/pc/impls/hypre/hypre.o
C:\cygwin64\home\DANIEL~1\PETSC_~1.1\src\ksp\pc\impls\hypre\hypre.c(444,29):
error: assigning to 'hypre_Error' from incompatible type 'int'
hypre__global_error = 0;
^ ~
C:\cygwin64\home\DANIEL~1\PETSC_~1.1\include\petscerror.h(1752,7): note:
expanded from macro 'PetscStackCallExternalVoid'
__VA_ARGS__; \
^~~~~~~~~~~
C:\cygwin64\home\DANIEL~1\PETSC_~1.1\src\ksp\pc\impls\hypre\hypre.c(634,29):
error: assigning to 'hypre_Error' from incompatible type 'int'
hypre__global_error = 0;
^ ~
C:\cygwin64\home\DANIEL~1\PETSC_~1.1\include\petscerror.h(1752,7): note:
expanded from macro 'PetscStackCallExternalVoid'
__VA_ARGS__; \
^~~~~~~~~~~
2 errors generated.
make[3]: *** [gmakefile:195:
arch-mswin-c-opt/obj/ksp/pc/impls/hypre/hypre.o] Error 1
make[3]: *** Waiting for unfinished jobs....
FC arch-mswin-c-opt/obj/ksp/f90-mod/petsckspdefmod.o
CC arch-mswin-c-opt/obj/dm/impls/da/hypre/mhyp.o
CC arch-mswin-c-opt/obj/mat/impls/hypre/mhypre.o
make[3]: Leaving directory '/home/DanielOGS/petsc_ogs_3.19.1'
make[2]: *** [/home/DanielOGS/petsc_ogs_3.19.1/lib/petsc/conf/rules.doc:28:
libs] Error 2
make[2]: Leaving directory '/home/DanielOGS/petsc_ogs_3.19.1'
**************************ERROR*************************************
Error during compile, check arch-mswin-c-opt/lib/petsc/conf/make.log
Send it and arch-mswin-c-opt/lib/petsc/conf/configure.log to
petsc-maint at mcs.anl.gov
********************************************************************
Finishing make run at Wed, 19 Jul 2023 17:07:00 +0100
----------------------------------------
But wait - isn't this the compile stage, not the linking stage? This seems
to imply that I've made a hash of providing include file such that a
definition of "hypre_Error"
cannot be seen - unless I'm misinterpreting. Interesting note about Hypre
and include files - if built using configure and make, all the include
files are conviniently copied
into hypre/src/hypre/include. This is not done for a cmake build - I had to
do the copying myself. Maybe I missed one.
On shared vs. static - if there a clear way of telling which I've ended up
with? I've checked the cmakelists for hypre and this seems to imply that
not-shared is the default,
which I didn't change:
# Configuration options
option(HYPRE_ENABLE_SHARED "Build a shared library" OFF)
option(HYPRE_ENABLE_BIGINT "Use long long int for HYPRE_Int" OFF)
option(HYPRE_ENABLE_MIXEDINT "Use long long int for HYPRE_BigInt,
int for HYPRE_INT" OFF)
[....]
checking again, I've noticed that the way that the stub-test fails is
different depending on whether it's called from the config script or used
in isolation - more details on that soon.
Thanks again,
Daniel
On Wed, Jul 19, 2023 at 4:58 PM Satish Balay via petsc-users <
petsc-users at mcs.anl.gov> wrote:
> I think it should work with static libraries and 64bit compilers.
>
> That's how I think --download-f2cblaslapack [etc] work.
>
> Also it works with MS-MPI - even-though its a dll install, the library
> stub provides this symbol somehow..
>
> balay at ps5 /cygdrive/c/Program Files (x86)/Microsoft SDKs/MPI/Lib/x64
> $ nm -Ao msmpi.lib |grep " MPI_Init"
> msmpi.lib:msmpi.dll:0000000000000000 T MPI_Init
> msmpi.lib:msmpi.dll:0000000000000000 T MPI_Init_thread
> msmpi.lib:msmpi.dll:0000000000000000 T MPI_Initialized
>
> However - if the library symbol is somehow mangled - this configure mode
> of checking library functions will fail.
>
> Checking PETSc dll build:
>
> balay at ps5 ~/petsc/arch-ci-mswin-uni/lib
> $ nm -Ao libpetsc.lib |grep MatCreateSeqAIJWithArrays
> libpetsc.lib:libpetsc.dll:0000000000000000 I
> __imp_MatCreateSeqAIJWithArrays
> libpetsc.lib:libpetsc.dll:0000000000000000 T MatCreateSeqAIJWithArrays
>
> It also has the unmangled symbol - so I guess this mode can work generally
> with dlls.
>
> Satish
>
>
> On Wed, 19 Jul 2023, Barry Smith wrote:
>
> >
> > Satish,
> >
> > So it will always fail on Windows with Windows compilers (both with
> static and shared libraries)? Is this true for all PETSc external packages?
> If so, why does the installation documentation say that some external
> packages can work with Windows compilers? (Presumably PETSc cannot since
> the configure tests will fail).
> >
> > Barry
> >
> >
> > > On Jul 19, 2023, at 11:40 AM, Satish Balay <balay at mcs.anl.gov> wrote:
> > >
> > > BTW: Some explanation of configure:
> > >
> > > It attempts the following on linux:
> > >
> > >>>>>>>
> > > Source:
> > > #include "confdefs.h"
> > > #include "conffix.h"
> > > /* Override any gcc2 internal prototype to avoid an error. */
> > > char HYPRE_IJMatrixCreate();
> > > static void _check_HYPRE_IJMatrixCreate() { HYPRE_IJMatrixCreate(); }
> > >
> > > int main(void) {
> > > _check_HYPRE_IJMatrixCreate();
> > > return 0;
> > > }
> > > <<<<<<<
> > >
> > > Note - it does not include 'HYPRE.h' here - but redefines the
> prototype as 'char HYPRE_IJMatrixCreate();
> > >
> > > Compiling it manually:
> > >
> > >>>>>
> > > [balay at pj01 petsc]$ cat conftest.c
> > > char HYPRE_IJMatrixCreate();
> > > static void _check_HYPRE_IJMatrixCreate() { HYPRE_IJMatrixCreate(); }
> > >
> > > int main(void) {
> > > _check_HYPRE_IJMatrixCreate();
> > > return 0;
> > > }
> > > [balay at pj01 petsc]$ gcc -c conftest.c
> > > [balay at pj01 petsc]$ nm -Ao conftest.o |grep HYPRE_IJMatrixCreate
> > > conftest.o:0000000000000000 t _check_HYPRE_IJMatrixCreate
> > > conftest.o: U HYPRE_IJMatrixCreate
> > > [balay at pj01 petsc]$ nm -Ao arch-linux-c-debug/lib/libHYPRE.so |grep
> HYPRE_IJMatrixCreate
> > > arch-linux-c-debug/lib/libHYPRE.so:000000000007f2c2 T
> HYPRE_IJMatrixCreate
> > > [balay at pj01 petsc]$
> > > <<<<
> > >
> > > Here the "U HYPRE_IJMatrixCreate" in conftest.o matches "T
> HYPRE_IJMatrixCreate" in libHYPRE.so - so the "link" test in configure
> succeeds!
> > >
> > >>>>>>>
> > > [balay at pj01 petsc]$ gcc -o conftest conftest.o
> arch-linux-c-debug/lib/libHYPRE.so
> > > [balay at pj01 petsc]$ echo $?
> > > 0
> > > <<<<<
> > >
> > > On windows - [due to name mangling by cdecl/stdcall, (/MT vs /MD)
> etc..] - this might not match - resulting in link failures.
> > >
> > > Satish
> > >
> > >
> > > On Wed, 19 Jul 2023, Satish Balay via petsc-users wrote:
> > >
> > >> You could try skipping this test [and assume --with-hypre-include and
> --with-hypre-lib options are correct] - and see if this works.
> > >>
> > >> diff --git a/config/BuildSystem/config/packages/hypre.py
> b/config/BuildSystem/config/packages/hypre.py
> > >> index 5bc88322aa2..2d6c7932e17 100644
> > >> --- a/config/BuildSystem/config/packages/hypre.py
> > >> +++ b/config/BuildSystem/config/packages/hypre.py
> > >> @@ -11,7 +11,7 @@ class Configure(config.package.GNUPackage):
> > >> self.requiresversion = 1
> > >> self.gitcommit = 'v'+self.version
> > >> self.download = ['git://
> https://github.com/hypre-space/hypre','
> https://github.com/hypre-space/hypre/archive/'+self.gitcommit+'.tar.gz']
> > >> - self.functions = ['HYPRE_IJMatrixCreate']
> > >> + self.functions = []
> > >> self.includes = ['HYPRE.h']
> > >> self.liblist = [['libHYPRE.a']]
> > >> self.buildLanguages = ['C','Cxx']
> > >>
> > >>
> > >> Satish
> > >>
> > >>
> > >> On Wed, 19 Jul 2023, Barry Smith wrote:
> > >>
> > >>>
> > >>> You don't indicate what type of libraries you built hypre with;
> static or shared. My guess is you ended up with shared
> > >>>
> > >>> I think the answer to your difficulty is hidden in __cdecl (Satish
> will know much better than me). When you are looking for symbols in Windows
> shared libraries you have to prepend something to the function prototype to
> have it successfully found. For example the PETSc include files have these
> things __declspec(dllimport) The configure test fails because it does not
> provide the needed prototype. Likely you built PTScotch with static
> libraries so no problem.
> > >>>
> > >>> The simplest fix would be to build static hypre libraries. I think
> it is a major project to get PETSc configure and macro system to work
> properly with external packages that are in Windows shared libraries since
> more use of __declspec would be needed.
> > >>>
> > >>> Barry
> > >>>
> > >>> The PETSc installation instructions should probably say something
> about external packages with Windows shared libraries.
> > >>>
> > >>>
> > >>>
> > >>>
> > >>>
> > >>>
> > >>>
> > >>>> On Jul 19, 2023, at 10:52 AM, Daniel Stone <
> daniel.stone at opengosim.com> wrote:
> > >>>>
> > >>>> Hello,
> > >>>>
> > >>>> I'm working on getting a petsc build running on windows. One
> necessary package to include is Hypre. I've been able to build Hypre
> seperately using cmake, and confirmed that the library works
> > >>>> by setting up a VS project to run some of the example programs.
> > >>>>
> > >>>> My attempted petsc build is being done through cygwin. I've been
> able to (with varying degrees of difficulty), build a fairly plain petsc,
> and one that downloads and builds ptscotch (after some modifications
> > >>>> to both ptscotch and the config script). I am now attempting to
> include Hypre (using the --hypre-iclude and --hypre-lib flags, etc). Note
> that the same compilers are being used for both Hypre and for petsc
> > >>>> through cygwin - the new intel oneapi compilers (icx and ifx, after
> again varying amounts of pain to work around their awkwardness with the
> config script).
> > >>>>
> > >>>> I'm seeing a problem when the config script does some tests on the
> included hypre lib. The source code looks like:
> > >>>>
> > >>>> #include "confdefs.h"
> > >>>> #include "conffix.h"
> > >>>> /* Override any gcc2 internal prototype to avoid an error. */
> > >>>>
> > >>>> #include "HYPRE.h"
> > >>>>
> > >>>> char HYPRE_IJMatrixCreate();
> > >>>> static void _check_HYPRE_IJMatrixCreate() { HYPRE_IJMatrixCreate();
> }
> > >>>>
> > >>>> int main() {
> > >>>> _check_HYPRE_IJMatrixCreate();;
> > >>>> return 0;
> > >>>> }
> > >>>>
> > >>>>
> > >>>> As I understand this is a fairly standard type of stub program used
> by the config script to check that it is able to link to certain symbols in
> given libraries. Tests like this have succeeded in my builds that
> > >>>> include PTScotch.
> > >>>>
> > >>>> I keep getting a linker error with the above test, including if I
> seperate it out and try to build it seperately:
> > >>>>
> > >>>> unresolved external symbol "char __cdel HYPRE_IJMatrixCreate(void)"
> ....
> > >>>>
> > >>>> Ok, it looks like a problem with either the library or linker
> commands. But here's the interesting thing - If I transplant this code into
> VS, with the same project setting that allows it to build the much more
> > >>>> nontrivial Hypre example programs, I get the same error:
> > >>>>
> > >>>> Error LNK2001 unresolved external symbol "char __cdecl
> HYPRE_IJMatrixCreate(void)" (?HYPRE_IJMatrixCreate@@YADXZ) hypretry1
> C:\Users\DanielOGS\source\repos\hypretry1\hypretry1\Source.obj 1
> > >>>>
> > >>>> So it seems like there might be something about this type of stub
> program that is not working with my Hypre library. I don't fully understand
> this program - it's able to call the function with no arguments, but
> > >>>> it also needs to be linked against a library containing the
> function, apparently by wrapping it in a static void function? Not
> something I've seen before.
> > >>>>
> > >>>> Does anyone have any insight into what might be going wrong - or
> really just any explaination of how the stub program works so I can figure
> out why it isn't in this case?
> > >>>>
> > >>>> Many thanks,
> > >>>>
> > >>>> Daniel
> > >>>
> > >>>
> > >>
> > >
> >
>
>
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