date:20181031

Re: [petsc-dev] Error running on Titan with GPUs & GNU

2018-10-31 Thread Karl Rupp via petsc-dev


Hi Mark,

ah, I was confused by the Python information at the beginning of 
configure.log. So it is picking up the correct compiler.


Have you tried uncommenting the check for GNU?

Best regards,
Karli


On 10/31/18 11:40 AM, Mark Adams wrote:
It looks like configure is not finding the correct cc. It does not seem 
hard to find.


06:37 master= /lustre/atlas/proj-shared/geo127/petsc$ cc --version
gcc (GCC) 6.3.0 20161221 (Cray Inc.)
Copyright (C) 2016 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

06:37 master= /lustre/atlas/proj-shared/geo127/petsc$ which cc
/opt/cray/craype/2.5.13/bin/cc
06:38 master= /lustre/atlas/proj-shared/geo127/petsc$ which gcc
/opt/gcc/6.3.0/bin/gcc


On Wed, Oct 31, 2018 at 6:34 AM Mark Adams > wrote:




On Wed, Oct 31, 2018 at 5:05 AM Karl Rupp mailto:r...@iue.tuwien.ac.at>> wrote:

Hi Mark,

please comment or remove lines 83 and 84 in
   config/BuildSystem/config/packages/cuda.py

Is there a compiler newer than GCC 4.3 available?


You mean 6.3?

06:33  ~$ module avail gcc

-
/opt/modulefiles -
gcc/4.8.1          gcc/4.9.3          gcc/6.1.0 
gcc/6.3.0(default) gcc/7.2.0
gcc/4.8.2          gcc/5.3.0          gcc/6.2.0          gcc/7.1.0 
         gcc/7.3.0



Best regards,
Karli



On 10/31/18 8:15 AM, Mark Adams via petsc-dev wrote:
 > After loading a cuda module ...
 >
 > On Wed, Oct 31, 2018 at 2:58 AM Mark Adams mailto:mfad...@lbl.gov>
 > >> wrote:
 >
 >     I get an error with --with-cuda=1
 >
 >     On Tue, Oct 30, 2018 at 4:44 PM Smith, Barry F.
mailto:bsm...@mcs.anl.gov>
 >     >>
wrote:
 >
 >         --with-cudac=1 should be --with-cuda=1
 >
 >
 >
 >          > On Oct 30, 2018, at 12:35 PM, Smith, Barry F. via
petsc-dev
 >         mailto:petsc-dev@mcs.anl.gov>
>>
wrote:
 >          >
 >          >
 >          >
 >          >> On Oct 29, 2018, at 8:09 PM, Mark Adams
mailto:mfad...@lbl.gov>
 >         >> wrote:
 >          >>
 >          >> And a debug build seems to work:
 >          >
 >          >    Well ok.
 >          >
 >          >    Are there newer versions of the Gnu compiler
for this
 >         system? Are there any other compilers on the system
that would
 >         likely be less buggy? IBM compilers? If this simple code
 >         generates a gross error with optimization who's to
say how many
 >         more subtle bugs may be induced in the library by the
buggy
 >         optimizer (there may be none but IMHO probability
says there
 >         will be others).
 >          >
 >          >    Is there any chance that valgrind runs on this
machine;
 >         you could run the optimized version through it and
see what it says.
 >          >
 >          >   Barry
 >          >
 >          >>
 >          >> 21:04 1 master=
/lustre/atlas/proj-shared/geo127/petsc$ make
 >   
  PETSC_DIR=/lustre/atlas/proj-shared/geo127/petsc_titan_dbg64idx_gnu_cuda

 >         PETSC_ARCH="" test
 >          >> Running test examples to verify correct installation
 >          >> Using
 >   
  PETSC_DIR=/lustre/atlas/proj-shared/geo127/petsc_titan_dbg64idx_gnu_cuda

 >         and PETSC_ARCH=
 >          >> ***Error detected during compile or
 >         link!***
 >          >> See
http://www.mcs.anl.gov/petsc/documentation/faq.html
 >          >>
 >   
  /lustre/atlas/proj-shared/geo127/petsc/src/snes/examples/tutorials

 >         ex19
 >          >>
 >   
  *

 >          >> cc -o ex19.o -c -g
 > 
  -I/lustre/atlas/proj-shared/geo127/petsc_titan_dbg64idx_gnu_cuda/include    `pwd`/ex19.c

 >          >> cc -g  -o ex19 ex19.o
 >   
  -L/lustre/atlas/proj-shared/geo127/petsc_titan_dbg64idx_gnu_cuda/lib
 >   
  -Wl,-rpath,/lustre/atl

Re: [petsc-dev] Error running on Titan with GPUs & GNU

2018-10-31 Thread Mark Adams via petsc-dev

It looks like configure is not finding the correct cc. It does not seem
hard to find.

06:37 master= /lustre/atlas/proj-shared/geo127/petsc$ cc --version
gcc (GCC) 6.3.0 20161221 (Cray Inc.)
Copyright (C) 2016 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

06:37 master= /lustre/atlas/proj-shared/geo127/petsc$ which cc
/opt/cray/craype/2.5.13/bin/cc
06:38 master= /lustre/atlas/proj-shared/geo127/petsc$ which gcc
/opt/gcc/6.3.0/bin/gcc


On Wed, Oct 31, 2018 at 6:34 AM Mark Adams  wrote:

>
>
> On Wed, Oct 31, 2018 at 5:05 AM Karl Rupp  wrote:
>
>> Hi Mark,
>>
>> please comment or remove lines 83 and 84 in
>>   config/BuildSystem/config/packages/cuda.py
>>
>> Is there a compiler newer than GCC 4.3 available?
>>
>
> You mean 6.3?
>
> 06:33  ~$ module avail gcc
>
> - /opt/modulefiles
> -
> gcc/4.8.1  gcc/4.9.3  gcc/6.1.0
> gcc/6.3.0(default) gcc/7.2.0
> gcc/4.8.2  gcc/5.3.0  gcc/6.2.0  gcc/7.1.0
>   gcc/7.3.0
>
>
>
>>
>> Best regards,
>> Karli
>>
>>
>>
>> On 10/31/18 8:15 AM, Mark Adams via petsc-dev wrote:
>> > After loading a cuda module ...
>> >
>> > On Wed, Oct 31, 2018 at 2:58 AM Mark Adams > > > wrote:
>> >
>> > I get an error with --with-cuda=1
>> >
>> > On Tue, Oct 30, 2018 at 4:44 PM Smith, Barry F. > > > wrote:
>> >
>> > --with-cudac=1 should be --with-cuda=1
>> >
>> >
>> >
>> >  > On Oct 30, 2018, at 12:35 PM, Smith, Barry F. via petsc-dev
>> > mailto:petsc-dev@mcs.anl.gov>> wrote:
>> >  >
>> >  >
>> >  >
>> >  >> On Oct 29, 2018, at 8:09 PM, Mark Adams > > > wrote:
>> >  >>
>> >  >> And a debug build seems to work:
>> >  >
>> >  >Well ok.
>> >  >
>> >  >Are there newer versions of the Gnu compiler for this
>> > system? Are there any other compilers on the system that would
>> > likely be less buggy? IBM compilers? If this simple code
>> > generates a gross error with optimization who's to say how many
>> > more subtle bugs may be induced in the library by the buggy
>> > optimizer (there may be none but IMHO probability says there
>> > will be others).
>> >  >
>> >  >Is there any chance that valgrind runs on this machine;
>> > you could run the optimized version through it and see what it
>> says.
>> >  >
>> >  >   Barry
>> >  >
>> >  >>
>> >  >> 21:04 1 master= /lustre/atlas/proj-shared/geo127/petsc$ make
>> >
>>  PETSC_DIR=/lustre/atlas/proj-shared/geo127/petsc_titan_dbg64idx_gnu_cuda
>> > PETSC_ARCH="" test
>> >  >> Running test examples to verify correct installation
>> >  >> Using
>> >
>>  PETSC_DIR=/lustre/atlas/proj-shared/geo127/petsc_titan_dbg64idx_gnu_cuda
>> > and PETSC_ARCH=
>> >  >> ***Error detected during compile or
>> > link!***
>> >  >> See http://www.mcs.anl.gov/petsc/documentation/faq.html
>> >  >>
>> >
>>  /lustre/atlas/proj-shared/geo127/petsc/src/snes/examples/tutorials
>> > ex19
>> >  >>
>> >
>>  
>> *
>> >  >> cc -o ex19.o -c -g
>> >
>>  -I/lustre/atlas/proj-shared/geo127/petsc_titan_dbg64idx_gnu_cuda/include
>>   `pwd`/ex19.c
>> >  >> cc -g  -o ex19 ex19.o
>> >
>>  -L/lustre/atlas/proj-shared/geo127/petsc_titan_dbg64idx_gnu_cuda/lib
>> >
>>  
>> -Wl,-rpath,/lustre/atlas/proj-shared/geo127/petsc_titan_dbg64idx_gnu_cuda/lib
>> >
>>  -L/lustre/atlas/proj-shared/geo127/petsc_titan_dbg64idx_gnu_cuda/lib
>> > -lpetsc -lHYPRE -lflapack -lfblas -lparmetis -lmetis -ldl
>> >  >>
>> >
>>  
>> /lustre/atlas/proj-shared/geo127/petsc_titan_dbg64idx_gnu_cuda/lib/libpetsc.a(dlimpl.o):
>> > In function `PetscDLOpen':
>> >  >>
>> >
>>  /lustre/atlas1/geo127/proj-shared/petsc/src/sys/dll/dlimpl.c:108: warning:
>> > Using 'dlopen' in statically linked applications requires at
>> > runtime the shared libraries from the glibc version used for
>> linking
>> >  >>
>> >
>>  
>> /lustre/atlas/proj-shared/geo127/petsc_titan_dbg64idx_gnu_cuda/lib/libpetsc.a(send.o):
>> > In function `PetscOpenSocket':
>> >  >>
>> >
>>  
>> /lustre/atlas1/geo127/proj-shared/petsc/src/sys/classes/viewer/impls/socket/send.c:108:
>> > warning: Using 'gethostbyname' in statically linked applications
>> > requires at runtime the shared libraries from the glibc version
>> > used for linking
>> >  >> true ex19
>> >  >> rm

Re: [petsc-dev] Error running on Titan with GPUs & GNU

2018-10-31 Thread Mark Adams via petsc-dev

On Wed, Oct 31, 2018 at 5:05 AM Karl Rupp  wrote:

> Hi Mark,
>
> please comment or remove lines 83 and 84 in
>   config/BuildSystem/config/packages/cuda.py
>
> Is there a compiler newer than GCC 4.3 available?
>

You mean 6.3?

06:33  ~$ module avail gcc

- /opt/modulefiles
-
gcc/4.8.1  gcc/4.9.3  gcc/6.1.0  gcc/6.3.0(default)
gcc/7.2.0
gcc/4.8.2  gcc/5.3.0  gcc/6.2.0  gcc/7.1.0
gcc/7.3.0



>
> Best regards,
> Karli
>
>
>
> On 10/31/18 8:15 AM, Mark Adams via petsc-dev wrote:
> > After loading a cuda module ...
> >
> > On Wed, Oct 31, 2018 at 2:58 AM Mark Adams  > > wrote:
> >
> > I get an error with --with-cuda=1
> >
> > On Tue, Oct 30, 2018 at 4:44 PM Smith, Barry F.  > > wrote:
> >
> > --with-cudac=1 should be --with-cuda=1
> >
> >
> >
> >  > On Oct 30, 2018, at 12:35 PM, Smith, Barry F. via petsc-dev
> > mailto:petsc-dev@mcs.anl.gov>> wrote:
> >  >
> >  >
> >  >
> >  >> On Oct 29, 2018, at 8:09 PM, Mark Adams  > > wrote:
> >  >>
> >  >> And a debug build seems to work:
> >  >
> >  >Well ok.
> >  >
> >  >Are there newer versions of the Gnu compiler for this
> > system? Are there any other compilers on the system that would
> > likely be less buggy? IBM compilers? If this simple code
> > generates a gross error with optimization who's to say how many
> > more subtle bugs may be induced in the library by the buggy
> > optimizer (there may be none but IMHO probability says there
> > will be others).
> >  >
> >  >Is there any chance that valgrind runs on this machine;
> > you could run the optimized version through it and see what it
> says.
> >  >
> >  >   Barry
> >  >
> >  >>
> >  >> 21:04 1 master= /lustre/atlas/proj-shared/geo127/petsc$ make
> >
>  PETSC_DIR=/lustre/atlas/proj-shared/geo127/petsc_titan_dbg64idx_gnu_cuda
> > PETSC_ARCH="" test
> >  >> Running test examples to verify correct installation
> >  >> Using
> >
>  PETSC_DIR=/lustre/atlas/proj-shared/geo127/petsc_titan_dbg64idx_gnu_cuda
> > and PETSC_ARCH=
> >  >> ***Error detected during compile or
> > link!***
> >  >> See http://www.mcs.anl.gov/petsc/documentation/faq.html
> >  >>
> >
>  /lustre/atlas/proj-shared/geo127/petsc/src/snes/examples/tutorials
> > ex19
> >  >>
> >
>  
> *
> >  >> cc -o ex19.o -c -g
> >
>  -I/lustre/atlas/proj-shared/geo127/petsc_titan_dbg64idx_gnu_cuda/include
>   `pwd`/ex19.c
> >  >> cc -g  -o ex19 ex19.o
> >
>  -L/lustre/atlas/proj-shared/geo127/petsc_titan_dbg64idx_gnu_cuda/lib
> >
>  -Wl,-rpath,/lustre/atlas/proj-shared/geo127/petsc_titan_dbg64idx_gnu_cuda/lib
> >
>  -L/lustre/atlas/proj-shared/geo127/petsc_titan_dbg64idx_gnu_cuda/lib
> > -lpetsc -lHYPRE -lflapack -lfblas -lparmetis -lmetis -ldl
> >  >>
> >
>  
> /lustre/atlas/proj-shared/geo127/petsc_titan_dbg64idx_gnu_cuda/lib/libpetsc.a(dlimpl.o):
> > In function `PetscDLOpen':
> >  >>
> >
>  /lustre/atlas1/geo127/proj-shared/petsc/src/sys/dll/dlimpl.c:108: warning:
> > Using 'dlopen' in statically linked applications requires at
> > runtime the shared libraries from the glibc version used for
> linking
> >  >>
> >
>  
> /lustre/atlas/proj-shared/geo127/petsc_titan_dbg64idx_gnu_cuda/lib/libpetsc.a(send.o):
> > In function `PetscOpenSocket':
> >  >>
> >
>  
> /lustre/atlas1/geo127/proj-shared/petsc/src/sys/classes/viewer/impls/socket/send.c:108:
> > warning: Using 'gethostbyname' in statically linked applications
> > requires at runtime the shared libraries from the glibc version
> > used for linking
> >  >> true ex19
> >  >> rm ex19.o
> >  >> Possible error running C/C++
> > src/snes/examples/tutorials/ex19 with 1 MPI process
> >  >> See http://www.mcs.anl.gov/petsc/documentation/faq.html
> >  >> lid velocity = 0.0016, prandtl # = 1., grashof # = 1.
> >  >> Number of SNES iterations = 2
> >  >> Application 19081049 resources: utime ~1s, stime ~1s, Rss
> > ~17112, inblocks ~36504, outblocks ~111043
> >  >> Possible error running C/C++
> > src/snes/examples/tutorials/ex19 with 2 MPI processes
> >  >> See http://www.mcs.anl.gov/petsc/documentation/faq.html
> >  >> lid velocity = 0.0016, prandtl # = 1., grashof # = 1.
> >  >> Number of SNES iterations = 2
> >  >> Application 19081

Re: [petsc-dev] Error running on Titan with GPUs & GNU

2018-10-31 Thread Karl Rupp via petsc-dev


Hi Mark,

please comment or remove lines 83 and 84 in
 config/BuildSystem/config/packages/cuda.py

Is there a compiler newer than GCC 4.3 available?

Best regards,
Karli



On 10/31/18 8:15 AM, Mark Adams via petsc-dev wrote:

After loading a cuda module ...

On Wed, Oct 31, 2018 at 2:58 AM Mark Adams > wrote:


I get an error with --with-cuda=1

On Tue, Oct 30, 2018 at 4:44 PM Smith, Barry F. mailto:bsm...@mcs.anl.gov>> wrote:

--with-cudac=1 should be --with-cuda=1



 > On Oct 30, 2018, at 12:35 PM, Smith, Barry F. via petsc-dev
mailto:petsc-dev@mcs.anl.gov>> wrote:
 >
 >
 >
 >> On Oct 29, 2018, at 8:09 PM, Mark Adams mailto:mfad...@lbl.gov>> wrote:
 >>
 >> And a debug build seems to work:
 >
 >    Well ok.
 >
 >    Are there newer versions of the Gnu compiler for this
system? Are there any other compilers on the system that would
likely be less buggy? IBM compilers? If this simple code
generates a gross error with optimization who's to say how many
more subtle bugs may be induced in the library by the buggy
optimizer (there may be none but IMHO probability says there
will be others).
 >
 >    Is there any chance that valgrind runs on this machine;
you could run the optimized version through it and see what it says.
 >
 >   Barry
 >
 >>
 >> 21:04 1 master= /lustre/atlas/proj-shared/geo127/petsc$ make
PETSC_DIR=/lustre/atlas/proj-shared/geo127/petsc_titan_dbg64idx_gnu_cuda
PETSC_ARCH="" test
 >> Running test examples to verify correct installation
 >> Using
PETSC_DIR=/lustre/atlas/proj-shared/geo127/petsc_titan_dbg64idx_gnu_cuda
and PETSC_ARCH=
 >> ***Error detected during compile or
link!***
 >> See http://www.mcs.anl.gov/petsc/documentation/faq.html
 >>
/lustre/atlas/proj-shared/geo127/petsc/src/snes/examples/tutorials
ex19
 >>

*
 >> cc -o ex19.o -c -g 
  -I/lustre/atlas/proj-shared/geo127/petsc_titan_dbg64idx_gnu_cuda/include    `pwd`/ex19.c
 >> cc -g  -o ex19 ex19.o 
-L/lustre/atlas/proj-shared/geo127/petsc_titan_dbg64idx_gnu_cuda/lib


-Wl,-rpath,/lustre/atlas/proj-shared/geo127/petsc_titan_dbg64idx_gnu_cuda/lib
-L/lustre/atlas/proj-shared/geo127/petsc_titan_dbg64idx_gnu_cuda/lib
-lpetsc -lHYPRE -lflapack -lfblas -lparmetis -lmetis -ldl
 >>

/lustre/atlas/proj-shared/geo127/petsc_titan_dbg64idx_gnu_cuda/lib/libpetsc.a(dlimpl.o):
In function `PetscDLOpen':
 >>
/lustre/atlas1/geo127/proj-shared/petsc/src/sys/dll/dlimpl.c:108: 
warning:
Using 'dlopen' in statically linked applications requires at
runtime the shared libraries from the glibc version used for linking
 >>

/lustre/atlas/proj-shared/geo127/petsc_titan_dbg64idx_gnu_cuda/lib/libpetsc.a(send.o):
In function `PetscOpenSocket':
 >>

/lustre/atlas1/geo127/proj-shared/petsc/src/sys/classes/viewer/impls/socket/send.c:108:
warning: Using 'gethostbyname' in statically linked applications
requires at runtime the shared libraries from the glibc version
used for linking
 >> true ex19
 >> rm ex19.o
 >> Possible error running C/C++
src/snes/examples/tutorials/ex19 with 1 MPI process
 >> See http://www.mcs.anl.gov/petsc/documentation/faq.html
 >> lid velocity = 0.0016, prandtl # = 1., grashof # = 1.
 >> Number of SNES iterations = 2
 >> Application 19081049 resources: utime ~1s, stime ~1s, Rss
~17112, inblocks ~36504, outblocks ~111043
 >> Possible error running C/C++
src/snes/examples/tutorials/ex19 with 2 MPI processes
 >> See http://www.mcs.anl.gov/petsc/documentation/faq.html
 >> lid velocity = 0.0016, prandtl # = 1., grashof # = 1.
 >> Number of SNES iterations = 2
 >> Application 19081050 resources: utime ~1s, stime ~1s, Rss
~19816, inblocks ~36527, outblocks ~111043
 >> 5a6
 >>> Application 19081051 resources: utime ~1s, stime ~0s, Rss
~13864, inblocks ~36527, outblocks ~111043
 >>
/lustre/atlas/proj-shared/geo127/petsc/src/snes/examples/tutorials
 >> Possible problem with ex19_hypre, diffs above
 >> =
 >> ***Error detected during compile or
link!***
 >> See http://www.mcs.anl.gov/petsc/documentation/faq.html
 >>
/lustre/atlas/proj-shared/geo127/petsc/src/snes/examples/tutorials
ex5f
 >> **

Re: [petsc-dev] Error running on Titan with GPUs & GNU

Re: [petsc-dev] Error running on Titan with GPUs & GNU

Re: [petsc-dev] Error running on Titan with GPUs & GNU

Re: [petsc-dev] Error running on Titan with GPUs & GNU

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