Re: [petsc-users] error when configuring petsc with Intel Compilers 2019 update 3
Please be aware that Intel MPI 2019 u3 has a lot of bugs when you look into
a bug. You better upgrade Intel Parallel Studio to the latest version.
--Junchao Zhang
On Tue, May 26, 2020 at 2:41 PM Alfredo Jaramillo
wrote:
> Thanks for the tip! I will look into it.
>
> regards
> Alfredo
>
>
> On Tue, May 26, 2020 at 4:39 PM Matthew Knepley wrote:
>
>> On Tue, May 26, 2020 at 3:15 PM Alfredo Jaramillo <
>> ajaramillopa...@gmail.com> wrote:
>>
>>> Thank you Matthew!
>>>
>>> I need this version to work on my computer in order to look for a bug
>>> that appears in a cluster.
>>> I'm not sure how to make it work, I will try with an older Linux
>>> distribution.
>>>
>>
>> If you are just looking for a bug, maybe a Docker container would allow
>> easier experimentation?
>>
>> Thanks,
>>
>> Matt
>>
>>
>>> regards
>>> Alfredo
>>>
>>> On Tue, May 26, 2020 at 1:02 PM Matthew Knepley
>>> wrote:
>>>
On Tue, May 26, 2020 at 11:23 AM Alfredo Jaramillo <
ajaramillopa...@gmail.com> wrote:
> hello dear PETSc team,
>
> I'm trying to install PETSc with the 2019 update 3 Intel Parallel
> Studio. When starting the configuration process there appears the next
> message:
>
>
>
>
>
>
>
> *TESTING: checkFortran90Array from
> config.compilersFortran(/opt/petsc-3.13.0/config/BuildSystem/config/compilersFortran.py:211)***
>UNABLE to CONFIGURE with GIVEN OPTIONS(see configure.log for
> details):---Could
> not check Fortran pointer
> arguments
>
> the configuration log is attached to this message
>
> I would be very thankful of any kind help on this matter
>
It seems like headers in /usr/include are conflicting with your new
compiler.
Executing: mpiicc -c -o
/tmp/petsc-n__j58ih/config.compilersFortran/conftest.o
-I/tmp/petsc-n__j58ih/config.libraries
-I/tmp/petsc-n__j58ih/config.setCompilers
-I/tmp/petsc-n__j58ih/config.compilers
-I/tmp/petsc-n__j58ih/config.utilities.closure
-I/tmp/petsc-n__j58ih/config.compilersFortran -fPIC -O3 -march=native
-mtune=native /tmp/petsc-n__j58ih/config.compilersFortran/conftest.c
Possible ERROR while running compiler: exit code 2
stderr:
In file included from /usr/include/bits/floatn.h(119),
from /usr/include/stdlib.h(55),
from
/tmp/petsc-n__j58ih/config.compilersFortran/conftest.c(4):
/usr/include/bits/floatn-common.h(214): error: invalid combination of
type specifiers
typedef float _Float32;
^
In file included from /usr/include/bits/floatn.h(119),
from /usr/include/stdlib.h(55),
from
/tmp/petsc-n__j58ih/config.compilersFortran/conftest.c(4):
/usr/include/bits/floatn-common.h(251): error: invalid combination of
type specifiers
typedef double _Float64;
^
In file included from /usr/include/bits/floatn.h(119),
from /usr/include/stdlib.h(55),
from
/tmp/petsc-n__j58ih/config.compilersFortran/conftest.c(4):
/usr/include/bits/floatn-common.h(268): error: invalid combination of
type specifiers
typedef double _Float32x;
^
In file included from /usr/include/bits/floatn.h(119),
from /usr/include/stdlib.h(55),
from
/tmp/petsc-n__j58ih/config.compilersFortran/conftest.c(4):
/usr/include/bits/floatn-common.h(285): error: invalid combination of
type specifiers
typedef long double _Float64x;
^
compilation aborted for
/tmp/petsc-n__j58ih/config.compilersFortran/conftest.c (code 2)
Source:
#include "confdefs.h"
#include "conffix.h"
#include
#include
void f90arraytest_(void* a1, void* a2,void* a3, void* i)
{
printf("arrays [%p %p %p]\n",a1,a2,a3);
fflush(stdout);
return;
}
void f90ptrtest_(void* a1, void* a2,void* a3, void* i, void* p1 ,void*
p2, void* p3)
{
printf("arrays [%p %p %p]\n",a1,a2,a3);
if ((p1 == p3) && (p1 != p2)) {
printf("pointers match! [%p %p] [%p]\n",p1,p3,p2);
fflush(stdout);
} else {
printf("pointers do not match! [%p %p] [%p]\n",p1,p3,p2);
fflush(stdout);
exit(111);
}
return;
}
Thanks,
Matt
Alfredo
>
--
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
Re: [petsc-users] error when configuring petsc with Intel Compilers 2019 update 3
Thank you Matthew!
I need this version to work on my computer in order to look for a bug that
appears in a cluster.
I'm not sure how to make it work, I will try with an older Linux
distribution.
regards
Alfredo
On Tue, May 26, 2020 at 1:02 PM Matthew Knepley wrote:
> On Tue, May 26, 2020 at 11:23 AM Alfredo Jaramillo <
> ajaramillopa...@gmail.com> wrote:
>
>> hello dear PETSc team,
>>
>> I'm trying to install PETSc with the 2019 update 3 Intel Parallel Studio.
>> When starting the configuration process there appears the next message:
>>
>>
>>
>>
>>
>>
>>
>> *TESTING: checkFortran90Array from
>> config.compilersFortran(/opt/petsc-3.13.0/config/BuildSystem/config/compilersFortran.py:211)***
>>UNABLE to CONFIGURE with GIVEN OPTIONS(see configure.log for
>> details):---Could
>> not check Fortran pointer
>> arguments
>>
>> the configuration log is attached to this message
>>
>> I would be very thankful of any kind help on this matter
>>
>
> It seems like headers in /usr/include are conflicting with your new
> compiler.
>
> Executing: mpiicc -c -o
> /tmp/petsc-n__j58ih/config.compilersFortran/conftest.o
> -I/tmp/petsc-n__j58ih/config.libraries
> -I/tmp/petsc-n__j58ih/config.setCompilers
> -I/tmp/petsc-n__j58ih/config.compilers
> -I/tmp/petsc-n__j58ih/config.utilities.closure
> -I/tmp/petsc-n__j58ih/config.compilersFortran -fPIC -O3 -march=native
> -mtune=native /tmp/petsc-n__j58ih/config.compilersFortran/conftest.c
> Possible ERROR while running compiler: exit code 2
> stderr:
> In file included from /usr/include/bits/floatn.h(119),
> from /usr/include/stdlib.h(55),
> from
> /tmp/petsc-n__j58ih/config.compilersFortran/conftest.c(4):
> /usr/include/bits/floatn-common.h(214): error: invalid combination of type
> specifiers
> typedef float _Float32;
> ^
>
> In file included from /usr/include/bits/floatn.h(119),
> from /usr/include/stdlib.h(55),
> from
> /tmp/petsc-n__j58ih/config.compilersFortran/conftest.c(4):
> /usr/include/bits/floatn-common.h(251): error: invalid combination of type
> specifiers
> typedef double _Float64;
> ^
>
> In file included from /usr/include/bits/floatn.h(119),
> from /usr/include/stdlib.h(55),
> from
> /tmp/petsc-n__j58ih/config.compilersFortran/conftest.c(4):
> /usr/include/bits/floatn-common.h(268): error: invalid combination of type
> specifiers
> typedef double _Float32x;
> ^
>
> In file included from /usr/include/bits/floatn.h(119),
> from /usr/include/stdlib.h(55),
> from
> /tmp/petsc-n__j58ih/config.compilersFortran/conftest.c(4):
> /usr/include/bits/floatn-common.h(285): error: invalid combination of type
> specifiers
> typedef long double _Float64x;
> ^
>
> compilation aborted for
> /tmp/petsc-n__j58ih/config.compilersFortran/conftest.c (code 2)
> Source:
> #include "confdefs.h"
> #include "conffix.h"
> #include
> #include
> void f90arraytest_(void* a1, void* a2,void* a3, void* i)
> {
> printf("arrays [%p %p %p]\n",a1,a2,a3);
> fflush(stdout);
> return;
> }
> void f90ptrtest_(void* a1, void* a2,void* a3, void* i, void* p1 ,void* p2,
> void* p3)
> {
> printf("arrays [%p %p %p]\n",a1,a2,a3);
> if ((p1 == p3) && (p1 != p2)) {
> printf("pointers match! [%p %p] [%p]\n",p1,p3,p2);
> fflush(stdout);
> } else {
> printf("pointers do not match! [%p %p] [%p]\n",p1,p3,p2);
> fflush(stdout);
> exit(111);
> }
> return;
> }
>
> Thanks,
>
> Matt
>
> Alfredo
>>
> --
> 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/
>
Re: [petsc-users] error when configuring petsc with Intel Compilers 2019 update 3
On Tue, May 26, 2020 at 11:23 AM Alfredo Jaramillo <
ajaramillopa...@gmail.com> wrote:
> hello dear PETSc team,
>
> I'm trying to install PETSc with the 2019 update 3 Intel Parallel Studio.
> When starting the configuration process there appears the next message:
>
>
>
>
>
>
>
> *TESTING: checkFortran90Array from
> config.compilersFortran(/opt/petsc-3.13.0/config/BuildSystem/config/compilersFortran.py:211)***
>UNABLE to CONFIGURE with GIVEN OPTIONS(see configure.log for
> details):---Could
> not check Fortran pointer
> arguments
>
> the configuration log is attached to this message
>
> I would be very thankful of any kind help on this matter
>
It seems like headers in /usr/include are conflicting with your new
compiler.
Executing: mpiicc -c -o
/tmp/petsc-n__j58ih/config.compilersFortran/conftest.o
-I/tmp/petsc-n__j58ih/config.libraries
-I/tmp/petsc-n__j58ih/config.setCompilers
-I/tmp/petsc-n__j58ih/config.compilers
-I/tmp/petsc-n__j58ih/config.utilities.closure
-I/tmp/petsc-n__j58ih/config.compilersFortran -fPIC -O3 -march=native
-mtune=native /tmp/petsc-n__j58ih/config.compilersFortran/conftest.c
Possible ERROR while running compiler: exit code 2
stderr:
In file included from /usr/include/bits/floatn.h(119),
from /usr/include/stdlib.h(55),
from
/tmp/petsc-n__j58ih/config.compilersFortran/conftest.c(4):
/usr/include/bits/floatn-common.h(214): error: invalid combination of type
specifiers
typedef float _Float32;
^
In file included from /usr/include/bits/floatn.h(119),
from /usr/include/stdlib.h(55),
from
/tmp/petsc-n__j58ih/config.compilersFortran/conftest.c(4):
/usr/include/bits/floatn-common.h(251): error: invalid combination of type
specifiers
typedef double _Float64;
^
In file included from /usr/include/bits/floatn.h(119),
from /usr/include/stdlib.h(55),
from
/tmp/petsc-n__j58ih/config.compilersFortran/conftest.c(4):
/usr/include/bits/floatn-common.h(268): error: invalid combination of type
specifiers
typedef double _Float32x;
^
In file included from /usr/include/bits/floatn.h(119),
from /usr/include/stdlib.h(55),
from
/tmp/petsc-n__j58ih/config.compilersFortran/conftest.c(4):
/usr/include/bits/floatn-common.h(285): error: invalid combination of type
specifiers
typedef long double _Float64x;
^
compilation aborted for
/tmp/petsc-n__j58ih/config.compilersFortran/conftest.c (code 2)
Source:
#include "confdefs.h"
#include "conffix.h"
#include
#include
void f90arraytest_(void* a1, void* a2,void* a3, void* i)
{
printf("arrays [%p %p %p]\n",a1,a2,a3);
fflush(stdout);
return;
}
void f90ptrtest_(void* a1, void* a2,void* a3, void* i, void* p1 ,void* p2,
void* p3)
{
printf("arrays [%p %p %p]\n",a1,a2,a3);
if ((p1 == p3) && (p1 != p2)) {
printf("pointers match! [%p %p] [%p]\n",p1,p3,p2);
fflush(stdout);
} else {
printf("pointers do not match! [%p %p] [%p]\n",p1,p3,p2);
fflush(stdout);
exit(111);
}
return;
}
Thanks,
Matt
Alfredo
>
--
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/
