SIG_SETMASK undeclared error while building parallel version with cygwin

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SIG_SETMASK undeclared error while building parallel version with cygwin

kostas syranidis
Dear all,

I hope I am referring to the correct hdf community.

I recently attempted to install parallel hdf5-1.10.1 from source in cygwin and stumbled into a SIG_SETMASK undeclared error during make.

In general I tried to follow the instructions from https://support.hdfgroup.org/ftp/HDF5/current/src/unpacked/release_docs/INSTALL_parallel

First I run the c version of the Sample_mpio.c and I suppose it worked:
Proc 2: all tests passed
Proc 3: all tests passed
Proc 1: all tests passed
Proc 0: all tests passed


Then I tried:
CC=mpicc ./configure --enable-parallel --enable-shared

and then make 

but at some point it exited with this

"SIG_SETMASK undeclared ... #define HDsigsetjmp(J,N) sigsetjmp(J,N) ... in expansion of macro ..."

error.

Since there are no separate instructions for cygwin, like for the serial case, I thought it might be an issue of cygwin. Does anyone know how to fix this?

One last question about the installation is szip. I built from source into the home folder but I have not changed any path variables. Will hdf be able to find it or is it not important?

I use Windows 7 and cygwin 2.8.2.

Any help would be appreciated.

With kind regards,
Konstantinos Syranidis

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Re: SIG_SETMASK undeclared error while building parallel version with cygwin

marco atzeri-2
On 01/08/2017 17:02, kostas syranidis wrote:

> Dear all,
>
> I hope I am referring to the correct hdf community.
>
> I recently attempted to install parallel hdf5-1.10.1 from source in
> cygwin and stumbled into a SIG_SETMASK undeclared error during make.
>
> In general I tried to follow the instructions from
> https://support.hdfgroup.org/ftp/HDF5/current/src/unpacked/release_docs/INSTALL_parallel
> <https://support.hdfgroup.org/ftp/HDF5/current/src/unpacked/release_docs/INSTALL_parallel>
>
>
> First I run the c version of the Sample_mpio.c and I suppose it worked:
> Proc 2: all tests passed
> Proc 3: all tests passed
> Proc 1: all tests passed
> Proc 0: all tests passed
>
>
> Then I tried:
>
> CC=mpicc ./configure --enable-parallel --enable-shared
>
> and then make
>
> but at some point it exited with this
>
> "SIG_SETMASK undeclared ... #define HDsigsetjmp(J,N)  sigsetjmp(J,N) ... in expansion of macro ..."
>
> error.

the problem is not due to the --enable-parallel

Trying to rebuild the serial 1.8.18 I see the same issue,
so it is likely a consequence of changes in the cygwing headers.

>
> Since there are no separate instructions for cygwin, like for the serial case, I thought it might be an issue of cygwin. Does anyone know how to fix this?

I will look on that, but it could be in September

>
> One last question about the installation is szip. I built from source into the home folder but I have not changed any path variables. Will hdf be able to find it or is it not important?
>
> I use Windows 7 and cygwin 2.8.2.
>
>
> Any help would be appreciated.
>
> With kind regards,
>
> Konstantinos Syranidis
>

Regards
Marco

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Re: SIG_SETMASK undeclared error while building parallel version with cygwin

marco atzeri-2
On 05/08/2017 23:16, Marco Atzeri wrote:
> On 01/08/2017 17:02, kostas syranidis wrote:
>> Dear all,
>>

>> Then I tried:
>>
>> CC=mpicc ./configure --enable-parallel --enable-shared
>>
>> and then make
>>
>> but at some point it exited with this
>>
>> "SIG_SETMASK undeclared ... #define HDsigsetjmp(J,N)  sigsetjmp(J,N)
>> ... in expansion of macro ..."
>>
>> error.
>
> the problem is not due to the --enable-parallel
>
> Trying to rebuild the serial 1.8.18 I see the same issue,
> so it is likely a consequence of changes in the cygwing headers.
>

Kostas,
as workaround you can remove "-std=c99" from  config/gnu-flags

I raised the issue on the cygwin mailing list, as this is a
change from the recent past:

https://cygwin.com/ml/cygwin/2017-08/msg00060.html
https://cygwin.com/ml/cygwin-announce/2017-04/msg00033.html

Regards
Marco




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Re: SIG_SETMASK undeclared error while building parallel version with cygwin

marco atzeri-2
On 06/08/2017 11:12, Marco Atzeri wrote:

> On 05/08/2017 23:16, Marco Atzeri wrote:
>> On 01/08/2017 17:02, kostas syranidis wrote:
>>> Dear all,
>>>
>
>>> Then I tried:
>>>
>>> CC=mpicc ./configure --enable-parallel --enable-shared
>>>
>>> and then make
>>>
>>> but at some point it exited with this
>>>
>>> "SIG_SETMASK undeclared ... #define HDsigsetjmp(J,N)  sigsetjmp(J,N)
>>> ... in expansion of macro ..."
>>>
>>> error.
>>
>> the problem is not due to the --enable-parallel
>>
>> Trying to rebuild the serial 1.8.18 I see the same issue,
>> so it is likely a consequence of changes in the cygwing headers.
>>
>
> Kostas,
> as workaround you can remove "-std=c99" from  config/gnu-flags
>
> I raised the issue on the cygwin mailing list, as this is a
> change from the recent past:
>
> https://cygwin.com/ml/cygwin/2017-08/msg00060.html
> https://cygwin.com/ml/cygwin-announce/2017-04/msg00033.html
>
> Regards
> Marco
>

The change in cygwin headers is showing an inconsistency in the HDF5

sigsetjmp is not in C99 so putting in config/gnu-flags

H5_CFLAGS="$H5_CFLAGS $arch -std=c99 ...

should not enable the use of sigsetjmp at all.

https://cygwin.com/ml/cygwin/2017-08/msg00066.html



Regards
Marco





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Re: SIG_SETMASK undeclared error while building parallel version with cygwin

kostas syranidis
Dear Marco,

Thank you for the helpful comments. I also contacted the hdf support and apparently parallel hdf is not supported or tested for cygwin, therefore I expect that there might be more problems on the way.

Anyhow, I used make CFLAGS=-D_POSIX_C_SOURCE and this error does not appear anymore. However, "make check" gives a segmentation fault error for  testhdf5.exe.
I have also opened a thread in stackoverflow, if anyone would like to contribute.

Best,
Kostas

2017-08-07 0:01 GMT+02:00 Marco Atzeri <[hidden email]>:
On 06/08/2017 11:12, Marco Atzeri wrote:
On 05/08/2017 23:16, Marco Atzeri wrote:
On 01/08/2017 17:02, kostas syranidis wrote:
Dear all,


Then I tried:

CC=mpicc ./configure --enable-parallel --enable-shared

and then make

but at some point it exited with this

"SIG_SETMASK undeclared ... #define HDsigsetjmp(J,N)  sigsetjmp(J,N)
... in expansion of macro ..."

error.

the problem is not due to the --enable-parallel

Trying to rebuild the serial 1.8.18 I see the same issue,
so it is likely a consequence of changes in the cygwing headers.


Kostas,
as workaround you can remove "-std=c99" from  config/gnu-flags

I raised the issue on the cygwin mailing list, as this is a
change from the recent past:

https://cygwin.com/ml/cygwin/2017-08/msg00060.html
https://cygwin.com/ml/cygwin-announce/2017-04/msg00033.html

Regards
Marco


The change in cygwin headers is showing an inconsistency in the HDF5

sigsetjmp is not in C99 so putting in config/gnu-flags

H5_CFLAGS="$H5_CFLAGS $arch -std=c99 ...

should not enable the use of sigsetjmp at all.

https://cygwin.com/ml/cygwin/2017-08/msg00066.html



Regards
Marco





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