Re: [petsc-users] Can not configure PETSc-master with clang-3.9

[Satish Balay]

Ok - this is not clang from apple. So I guess it needs that extra 'xcode-select 
--install'

I don't think gcc from brew needed this. [And I don't remember if I checked 
clang from brew]

Satish


On Mon, 16 Oct 2017, Kong, Fande wrote:

> On Mon, Oct 16, 2017 at 12:07 PM, Satish Balay  wrote:
> 
> > BTW: Which clang are you using?
> >
> > mpicc -show
> >
> 
> 
> 
> mpicc -show
> 
> clang -Wl,-commons,use_dylibs
> -I/opt/moose/mpich/mpich-3.2/clang-opt/include
> -L/opt/moose/mpich/mpich-3.2/clang-opt/lib -lmpi -lpmpi
> 
> 
> 
> > mpicc --version
> >
> 
> mpicc -v
> 
> mpicc for MPICH version 3.2
> clang version 3.9.0 (tags/RELEASE_390/final)
> Target: x86_64-apple-darwin16.7.0
> Thread model: posix
> InstalledDir: /opt/moose/llvm-3.9.0/bin
> clang-3.9: warning: argument unused during compilation: '-I
> /opt/moose/mpich/mpich-3.2/clang-opt/include'
> 
> 
> I guess because we are using a customize installation of clang.
> 
> 
> Fande,
> 
> 
> >
> > Satish
> >
> > On Mon, 16 Oct 2017, Satish Balay wrote:
> >
> > > Thats weird.
> > >
> > > From what I can recall - some tools (like pgi compilers) need this -
> > > but the xcode compilers do not.
> > >
> > > Basically xcode clang can pick up includes from the xcode specific
> > > location - but other tools look for includes in /usr/incldue
> > >
> > > And 'xcode-select --install' adds the /usr/include etc links.
> > >
> > > Satish
> > >
> > >
> > > On Mon, 16 Oct 2017, Kong, Fande wrote:
> > >
> > > > Now it is working. It turns out I need to do something like
> > "xcode-select
> > > > --install" after upgrading OS, and of course we need to agree the
> > license.
> > > >
> > > >
> > > > Fande,
> > > >
> > > > On Mon, Oct 16, 2017 at 10:58 AM, Richard Tran Mills 
> > > > wrote:
> > > >
> > > > > Fande,
> > > > >
> > > > > Did you remember to agree to the XCode license after your upgrade,
> > if you
> > > > > did an XCode upgrade? You have to do the license agreement again,
> > otherwise
> > > > > the compilers don't work at all. Apologies if this seems like a
> > silly thing
> > > > > to ask, but this has caused me a few minutes of confusion before.
> > > > >
> > > > > --Richard
> > > > >
> > > > > On Mon, Oct 16, 2017 at 9:52 AM, Jed Brown  wrote:
> > > > >
> > > > >> "Kong, Fande"  writes:
> > > > >>
> > > > >> > Hi All,
> > > > >> >
> > > > >> > I just upgraded  MAC OS, and also updated all other related
> > packages.
> > > > >> Now
> > > > >> > I can not configure PETSc-master any more.
> > > > >>
> > > > >> Your compiler paths are broken.
> > > > >>
> > > > >> /var/folders/6q/y12qpzw12dg5qx5x96dd5_bhtzr4_y/T/petsc-
> > > > >> mFgio7/config.setCompilers/conftest.c:3:10: fatal error:
> > 'stdlib.h' file
> > > > >> not found
> > > > >> #include 
> > > > >>  ^
> > > > >> 1 error generated.
> > > > >>
> > > > >
> > > > >
> > > >
> > >
> > >
> >
> >
> 

Re: [petsc-users] Can not configure PETSc-master with clang-3.9

[Kong, Fande]

On Mon, Oct 16, 2017 at 12:07 PM, Satish Balay  wrote:

> BTW: Which clang are you using?
>
> mpicc -show
>



mpicc -show

clang -Wl,-commons,use_dylibs
-I/opt/moose/mpich/mpich-3.2/clang-opt/include
-L/opt/moose/mpich/mpich-3.2/clang-opt/lib -lmpi -lpmpi



> mpicc --version
>

mpicc -v

mpicc for MPICH version 3.2
clang version 3.9.0 (tags/RELEASE_390/final)
Target: x86_64-apple-darwin16.7.0
Thread model: posix
InstalledDir: /opt/moose/llvm-3.9.0/bin
clang-3.9: warning: argument unused during compilation: '-I
/opt/moose/mpich/mpich-3.2/clang-opt/include'


I guess because we are using a customize installation of clang.


Fande,


>
> Satish
>
> On Mon, 16 Oct 2017, Satish Balay wrote:
>
> > Thats weird.
> >
> > From what I can recall - some tools (like pgi compilers) need this -
> > but the xcode compilers do not.
> >
> > Basically xcode clang can pick up includes from the xcode specific
> > location - but other tools look for includes in /usr/incldue
> >
> > And 'xcode-select --install' adds the /usr/include etc links.
> >
> > Satish
> >
> >
> > On Mon, 16 Oct 2017, Kong, Fande wrote:
> >
> > > Now it is working. It turns out I need to do something like
> "xcode-select
> > > --install" after upgrading OS, and of course we need to agree the
> license.
> > >
> > >
> > > Fande,
> > >
> > > On Mon, Oct 16, 2017 at 10:58 AM, Richard Tran Mills 
> > > wrote:
> > >
> > > > Fande,
> > > >
> > > > Did you remember to agree to the XCode license after your upgrade,
> if you
> > > > did an XCode upgrade? You have to do the license agreement again,
> otherwise
> > > > the compilers don't work at all. Apologies if this seems like a
> silly thing
> > > > to ask, but this has caused me a few minutes of confusion before.
> > > >
> > > > --Richard
> > > >
> > > > On Mon, Oct 16, 2017 at 9:52 AM, Jed Brown  wrote:
> > > >
> > > >> "Kong, Fande"  writes:
> > > >>
> > > >> > Hi All,
> > > >> >
> > > >> > I just upgraded  MAC OS, and also updated all other related
> packages.
> > > >> Now
> > > >> > I can not configure PETSc-master any more.
> > > >>
> > > >> Your compiler paths are broken.
> > > >>
> > > >> /var/folders/6q/y12qpzw12dg5qx5x96dd5_bhtzr4_y/T/petsc-
> > > >> mFgio7/config.setCompilers/conftest.c:3:10: fatal error:
> 'stdlib.h' file
> > > >> not found
> > > >> #include 
> > > >>  ^
> > > >> 1 error generated.
> > > >>
> > > >
> > > >
> > >
> >
> >
>
>

Re: [petsc-users] Can not configure PETSc-master with clang-3.9

[Satish Balay]

BTW: Which clang are you using?

mpicc -show
mpicc --version

Satish

On Mon, 16 Oct 2017, Satish Balay wrote:

> Thats weird.
> 
> From what I can recall - some tools (like pgi compilers) need this -
> but the xcode compilers do not.
> 
> Basically xcode clang can pick up includes from the xcode specific
> location - but other tools look for includes in /usr/incldue
> 
> And 'xcode-select --install' adds the /usr/include etc links.
> 
> Satish
> 
> 
> On Mon, 16 Oct 2017, Kong, Fande wrote:
> 
> > Now it is working. It turns out I need to do something like "xcode-select
> > --install" after upgrading OS, and of course we need to agree the license.
> > 
> > 
> > Fande,
> > 
> > On Mon, Oct 16, 2017 at 10:58 AM, Richard Tran Mills 
> > wrote:
> > 
> > > Fande,
> > >
> > > Did you remember to agree to the XCode license after your upgrade, if you
> > > did an XCode upgrade? You have to do the license agreement again, 
> > > otherwise
> > > the compilers don't work at all. Apologies if this seems like a silly 
> > > thing
> > > to ask, but this has caused me a few minutes of confusion before.
> > >
> > > --Richard
> > >
> > > On Mon, Oct 16, 2017 at 9:52 AM, Jed Brown  wrote:
> > >
> > >> "Kong, Fande"  writes:
> > >>
> > >> > Hi All,
> > >> >
> > >> > I just upgraded  MAC OS, and also updated all other related packages.
> > >> Now
> > >> > I can not configure PETSc-master any more.
> > >>
> > >> Your compiler paths are broken.
> > >>
> > >> /var/folders/6q/y12qpzw12dg5qx5x96dd5_bhtzr4_y/T/petsc-
> > >> mFgio7/config.setCompilers/conftest.c:3:10: fatal error: 'stdlib.h' file
> > >> not found
> > >> #include 
> > >>  ^
> > >> 1 error generated.
> > >>
> > >
> > >
> > 
> 
> 

Re: [petsc-users] Can not configure PETSc-master with clang-3.9

[Kong, Fande]

Now it is working. It turns out I need to do something like "xcode-select
--install" after upgrading OS, and of course we need to agree the license.


Fande,

On Mon, Oct 16, 2017 at 10:58 AM, Richard Tran Mills 
wrote:

> Fande,
>
> Did you remember to agree to the XCode license after your upgrade, if you
> did an XCode upgrade? You have to do the license agreement again, otherwise
> the compilers don't work at all. Apologies if this seems like a silly thing
> to ask, but this has caused me a few minutes of confusion before.
>
> --Richard
>
> On Mon, Oct 16, 2017 at 9:52 AM, Jed Brown  wrote:
>
>> "Kong, Fande"  writes:
>>
>> > Hi All,
>> >
>> > I just upgraded  MAC OS, and also updated all other related packages.
>> Now
>> > I can not configure PETSc-master any more.
>>
>> Your compiler paths are broken.
>>
>> /var/folders/6q/y12qpzw12dg5qx5x96dd5_bhtzr4_y/T/petsc-
>> mFgio7/config.setCompilers/conftest.c:3:10: fatal error: 'stdlib.h' file
>> not found
>> #include 
>>  ^
>> 1 error generated.
>>
>
>

Re: [petsc-users] Can not configure PETSc-master with clang-3.9

[Richard Tran Mills]

Fande,

Did you remember to agree to the XCode license after your upgrade, if you
did an XCode upgrade? You have to do the license agreement again, otherwise
the compilers don't work at all. Apologies if this seems like a silly thing
to ask, but this has caused me a few minutes of confusion before.

--Richard

On Mon, Oct 16, 2017 at 9:52 AM, Jed Brown  wrote:

> "Kong, Fande"  writes:
>
> > Hi All,
> >
> > I just upgraded  MAC OS, and also updated all other related packages.
> Now
> > I can not configure PETSc-master any more.
>
> Your compiler paths are broken.
>
> /var/folders/6q/y12qpzw12dg5qx5x96dd5_bhtzr4_y/T/petsc-mFgio7/config.setCompilers/conftest.c:3:10:
> fatal error: 'stdlib.h' file not found
> #include 
>  ^
> 1 error generated.
>

Re: [petsc-users] Can not configure PETSc-master with clang-3.9

[Jed Brown]

"Kong, Fande"  writes:

> Hi All,
>
> I just upgraded  MAC OS, and also updated all other related packages.  Now
> I can not configure PETSc-master any more.

Your compiler paths are broken.

/var/folders/6q/y12qpzw12dg5qx5x96dd5_bhtzr4_y/T/petsc-mFgio7/config.setCompilers/conftest.c:3:10:
 fatal error: 'stdlib.h' file not found
#include 
 ^
1 error generated.

Re: [petsc-users] Can not configure PETSc-master with clang-3.9

[Matthew Knepley]

On Mon, Oct 16, 2017 at 12:07 PM, Kong, Fande  wrote:

> Hi All,
>
> I just upgraded  MAC OS, and also updated all other related packages.  Now
> I can not configure PETSc-master any more.
>
> See the attachment for more details.
>

Something is really wrong with your compilers

Source:
#include "confdefs.h"
#include "conffix.h"
#include 
Preprocess stderr before
filtering:/var/folders/6q/y12qpzw12dg5qx5x96dd5_bhtzr4_y/T/petsc-mFgio7/config.setCompilers/conftest.c:3:10:
fatal error: 'stdlib.h' file not found
#include 
 ^
1 error generated.
:

   Matt


>
>
> Fande,
>



-- 
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener

https://www.cse.buffalo.edu/~knepley/