Fix compiling issue with newer gcc-ng package versions

[CKehl]

@VictorOnink discovered an interesting bug.
On his cluster, he was running parcels and got the following error:

In file included from /tmp/parcels-20788/parcels_random_4145b686-38e2-45a1-aadd-d599bc75389a.c:1:0:
/home/ubelix/climate/vo18e689/anaconda3/envs/py3_parcels_v2_2/lib/python3.6/site-packages/parcels/include/parcels.h: In function 'temporal_interpolation_structured_grid':
/home/ubelix/climate/vo18e689/anaconda3/envs/py3_parcels_v2_2/lib/python3.6/site-packages/parcels/include/parcels.h:511:7: error: 'for' loop initial declarations are only allowed in C99 mode
       for (int i = 0; i < tii; i++) {                                   \
       ^
/home/ubelix/climate/vo18e689/anaconda3/envs/py3_parcels_v2_2/lib/python3.6/site-packages/parcels/include/parcels.h:544:7: note: in expansion of macro 'INTERP'
       INTERP(spatial_interpolation_bilinear, spatial_interpolation_trilinear_surface);
       ^
/home/ubelix/climate/vo18e689/anaconda3/envs/py3_parcels_v2_2/lib/python3.6/site-packages/parcels/include/parcels.h:511:7: note: use option -std=c99 or -std=gnu99 to compile your code
       for (int i = 0; i < tii; i++) {                                   \
       ^
/home/ubelix/climate/vo18e689/anaconda3/envs/py3_parcels_v2_2/lib/python3.6/site-packages/parcels/include/parcels.h:544:7: note: in expansion of macro 'INTERP'
       INTERP(spatial_interpolation_bilinear, spatial_interpolation_trilinear_surface);
       ^
/home/ubelix/climate/vo18e689/anaconda3/envs/py3_parcels_v2_2/lib/python3.6/site-packages/parcels/include/parcels.h:516:7: error: 'for' loop initial declarations are only allowed in C99 mode
       for (int i = 0; i < tii; i++) {                                   \
       ^
/home/ubelix/climate/vo18e689/anaconda3/envs/py3_parcels_v2_2/lib/python3.6/site-packages/parcels/include/parcels.h:544:7: note: in expansion of macro 'INTERP'
       INTERP(spatial_interpolation_bilinear, spatial_interpolation_trilinear_surface);
       ^
/home/ubelix/climate/vo18e689/anaconda3/envs/py3_parcels_v2_2/lib/python3.6/site-packages/parcels/include/parcels.h:511:7: error: 'for' loop initial declarations are only allowed in C99 mode
       for (int i = 0; i < tii; i++) {                                   \
       ^
/home/ubelix/climate/vo18e689/anaconda3/envs/py3_parcels_v2_2/lib/python3.6/site-packages/parcels/include/parcels.h:546:7: note: in expansion of macro 'INTERP'
       INTERP(spatial_interpolation_bilinear, spatial_interpolation_trilinear);
       ^
/home/ubelix/climate/vo18e689/anaconda3/envs/py3_parcels_v2_2/lib/python3.6/site-packages/parcels/include/parcels.h:516:7: error: 'for' loop initial declarations are only allowed in C99 mode
       for (int i = 0; i < tii; i++) {                                   \
       ^
/home/ubelix/climate/vo18e689/anaconda3/envs/py3_parcels_v2_2/lib/python3.6/site-packages/parcels/include/parcels.h:546:7: note: in expansion of macro 'INTERP'
       INTERP(spatial_interpolation_bilinear, spatial_interpolation_trilinear);
       ^
/home/ubelix/climate/vo18e689/anaconda3/envs/py3_parcels_v2_2/lib/python3.6/site-packages/parcels/include/parcels.h:511:7: error: 'for' loop initial declarations are only allowed in C99 mode
       for (int i = 0; i < tii; i++) {                                   \
       ^
/home/ubelix/climate/vo18e689/anaconda3/envs/py3_parcels_v2_2/lib/python3.6/site-packages/parcels/include/parcels.h:549:5: note: in expansion of macro 'INTERP'
     INTERP(spatial_interpolation_nearest2D, spatial_interpolation_nearest3D);
     ^
/home/ubelix/climate/vo18e689/anaconda3/envs/py3_parcels_v2_2/lib/python3.6/site-packages/parcels/include/parcels.h:516:7: error: 'for' loop initial declarations are only allowed in C99 mode
       for (int i = 0; i < tii; i++) {                                   \
       ^
/home/ubelix/climate/vo18e689/anaconda3/envs/py3_parcels_v2_2/lib/python3.6/site-packages/parcels/include/parcels.h:549:5: note: in expansion of macro 'INTERP'
     INTERP(spatial_interpolation_nearest2D, spatial_interpolation_nearest3D);
     ^
/home/ubelix/climate/vo18e689/anaconda3/envs/py3_parcels_v2_2/lib/python3.6/site-packages/parcels/include/parcels.h:511:7: error: 'for' loop initial declarations are only allowed in C99 mode
       for (int i = 0; i < tii; i++) {                                   \
       ^
/home/ubelix/climate/vo18e689/anaconda3/envs/py3_parcels_v2_2/lib/python3.6/site-packages/parcels/include/parcels.h:551:5: note: in expansion of macro 'INTERP'
     INTERP(spatial_interpolation_tracer_c_grid_2D, spatial_interpolation_tracer_c_grid_3D);
     ^
/home/ubelix/climate/vo18e689/anaconda3/envs/py3_parcels_v2_2/lib/python3.6/site-packages/parcels/include/parcels.h:516:7: error: 'for' loop initial declarations are only allowed in C99 mode
       for (int i = 0; i < tii; i++) {                                   \
       ^
/home/ubelix/climate/vo18e689/anaconda3/envs/py3_parcels_v2_2/lib/python3.6/site-packages/parcels/include/parcels.h:551:5: note: in expansion of macro 'INTERP'
     INTERP(spatial_interpolation_tracer_c_grid_2D, spatial_interpolation_tracer_c_grid_3D);
     ^
/home/ubelix/climate/vo18e689/anaconda3/envs/py3_parcels_v2_2/lib/python3.6/site-packages/parcels/include/parcels.h:511:7: error: 'for' loop initial declarations are only allowed in C99 mode
       for (int i = 0; i < tii; i++) {                                   \
       ^
/home/ubelix/climate/vo18e689/anaconda3/envs/py3_parcels_v2_2/lib/python3.6/site-packages/parcels/include/parcels.h:553:5: note: in expansion of macro 'INTERP'
     INTERP(spatial_interpolation_bilinear_invdist_land, spatial_interpolation_trilinear_invdist_land);
     ^
/home/ubelix/climate/vo18e689/anaconda3/envs/py3_parcels_v2_2/lib/python3.6/site-packages/parcels/include/parcels.h:516:7: error: 'for' loop initial declarations are only allowed in C99 mode
       for (int i = 0; i < tii; i++) {                                   \
       ^
/home/ubelix/climate/vo18e689/anaconda3/envs/py3_parcels_v2_2/lib/python3.6/site-packages/parcels/include/parcels.h:553:5: note: in expansion of macro 'INTERP'
     INTERP(spatial_interpolation_bilinear_invdist_land, spatial_interpolation_trilinear_invdist_land);
     ^
Compiling: gcc -Wall -fPIC -I/home/ubelix/climate/vo18e689/anaconda3/envs/py3_parcels_v2_2/lib/python3.6/site-packages/parcels/include -g -O3 -m64 -o /tmp/parcels-20788/parcels_random_4145b686-38e2-45a1-aadd-d599bc75389a.so /tmp/parcels-20788/parcels_random_4145b686-38e2-45a1-aadd-d599bc75389a.c -shared -m64

Now, we compared our version of gcc-ng. The outcome:
I have the package from the conda-forge channel, which gives us a gcc-version of 7.3.0. He has on the cluster a version of gcc with 9.3.0.

The issue is as follows:
gcc 9.3.0 is more strict in enforcing a certain C-standard during code-parsing. Now, having a for (...)-loop in a macro-definition is not allowed in the initial C-89 standard, which is the default standard applied by gcc without re-definition. gcc 7.3.0 doesn't check this part of the standard-compliance during the syntax check of C-parsing, but gcc 9.3.0 does check that compliance. Hence, we don't get an error with the conda-forge version of gcc-ng, but we do get that error with the anaconda version of gcc-ng.

How can we solve it ?

• add the compiler switch -std=c99 to the compiler (not linker) switches in the code generator in parcels

[erikvansebille]

Thanks for reporting! Could this be part of #914, which refactors the compiler? Would be a good application of why we need to soon merge that PR

[gmacgilchrist]

Just to flag that I also encountered this bug working on a cluster at GFDL. gcc version 9.3.0 is what was installed by default into the py3_parcels environment. A fresh install with gcc_linux-64==7.3.0 does not seem to have worked - same error crops up.

[gmacgilchrist]

Note that downgrading parcels to 2.1.5 works.

[CKehl]

Background on the compiler flag: see GCC man-page

[CKehl]

here is the related section about the applicable C-standard:

       -std=
           Determine the language standard.   This option is currently only supported when compiling C or C++.

           The compiler can accept several base standards, such as c90 or c++98, and GNU dialects of those standards, such as gnu90 or gnu++98.  When a base
           standard is specified, the compiler accepts all programs following that standard plus those using GNU extensions that do not contradict it.  For
           example, -std=c90 turns off certain features of GCC that are incompatible with ISO C90, such as the "asm" and "typeof" keywords, but not other
           GNU extensions that do not have a meaning in ISO C90, such as omitting the middle term of a "?:" expression. On the other hand, when a GNU
           dialect of a standard is specified, all features supported by the compiler are enabled, even when those features change the meaning of the base
           standard.  As a result, some strict-conforming programs may be rejected.  The particular standard is used by -Wpedantic to identify which
           features are GNU extensions given that version of the standard. For example -std=gnu90 -Wpedantic warns about C++ style // comments, while
           -std=gnu99 -Wpedantic does not.

           A value for this option must be provided; possible values are

           c90
           c89
           iso9899:1990
               Support all ISO C90 programs (certain GNU extensions that conflict with ISO C90 are disabled). Same as -ansi for C code.

           iso9899:199409
               ISO C90 as modified in amendment 1.

           c99
           c9x
           iso9899:1999
           iso9899:199x
               ISO C99.  This standard is substantially completely supported, modulo bugs and floating-point issues (mainly but not entirely relating to
               optional C99 features from Annexes F and G).  See <http://gcc.gnu.org/c99status.html> for more information.  The names c9x and iso9899:199x
               are deprecated.

           c11
           c1x
           iso9899:2011
               ISO C11, the 2011 revision of the ISO C standard.  This standard is substantially completely supported, modulo bugs, floating-point issues
               (mainly but not entirely relating to optional C11 features from Annexes F and G) and the optional Annexes K (Bounds-checking interfaces) and
               L (Analyzability).  The name c1x is deprecated.

           gnu90
           gnu89
               GNU dialect of ISO C90 (including some C99 features).

           gnu99
           gnu9x
               GNU dialect of ISO C99.  The name gnu9x is deprecated.

           gnu11
           gnu1x
               GNU dialect of ISO C11.  This is the default for C code.  The name gnu1x is deprecated. 

           c++98
           c++03
               The 1998 ISO C++ standard plus the 2003 technical corrigendum and some additional defect reports. Same as -ansi for C++ code.

           gnu++98
           gnu++03
               GNU dialect of -std=c++98.

           c++11
           c++0x
               The 2011 ISO C++ standard plus amendments.  The name c++0x is deprecated.

           gnu++11
           gnu++0x
               GNU dialect of -std=c++11.  The name gnu++0x is deprecated.

           c++14
           c++1y
               The 2014 ISO C++ standard plus amendments.  The name c++1y is deprecated.

           gnu++14
           gnu++1y
               GNU dialect of -std=c++14.  This is the default for C++ code.  The name gnu++1y is deprecated.

           c++1z
               The next revision of the ISO C++ standard, tentatively planned for 2017.  Support is highly experimental, and will almost certainly change in
               incompatible ways in future releases.

           gnu++1z
               GNU dialect of -std=c++1z.  Support is highly experimental, and will almost certainly change in incompatible ways in future releases.**

with GCC 8.4.0, this looks different:

       -std=
           Determine the language standard.   This option is currently only supported when compiling C or C++.

           The compiler can accept several base standards, such as c90 or c++98, and GNU dialects of those standards, such as gnu90 or gnu++98.  When a base
           standard is specified, the compiler accepts all programs following that standard plus those using GNU extensions that do not contradict it.  For
           example, -std=c90 turns off certain features of GCC that are incompatible with ISO C90, such as the "asm" and "typeof" keywords, but not other
           GNU extensions that do not have a meaning in ISO C90, such as omitting the middle term of a "?:" expression. On the other hand, when a GNU
           dialect of a standard is specified, all features supported by the compiler are enabled, even when those features change the meaning of the base
           standard.  As a result, some strict-conforming programs may be rejected.  The particular standard is used by -Wpedantic to identify which
           features are GNU extensions given that version of the standard. For example -std=gnu90 -Wpedantic warns about C++ style // comments, while
           -std=gnu99 -Wpedantic does not.

           A value for this option must be provided; possible values are

           c90
           c89
           iso9899:1990
               Support all ISO C90 programs (certain GNU extensions that conflict with ISO C90 are disabled). Same as -ansi for C code.

           iso9899:199409
               ISO C90 as modified in amendment 1.

           c99
           c9x
           iso9899:1999
           iso9899:199x
               ISO C99.  This standard is substantially completely supported, modulo bugs and floating-point issues (mainly but not entirely relating to
               optional C99 features from Annexes F and G).  See <http://gcc.gnu.org/c99status.html> for more information.  The names c9x and iso9899:199x
               are deprecated.

           c11
           c1x
           iso9899:2011
               ISO C11, the 2011 revision of the ISO C standard.  This standard is substantially completely supported, modulo bugs, floating-point issues
               (mainly but not entirely relating to optional C11 features from Annexes F and G) and the optional Annexes K (Bounds-checking interfaces) and
               L (Analyzability).  The name c1x is deprecated.

           c17
           c18
           iso9899:2017
           iso9899:2018
               ISO C17, the 2017 revision of the ISO C standard (expected to be published in 2018).  This standard is same as C11 except for corrections of
               defects (all of which are also applied with -std=c11) and a new value of "__STDC_VERSION__", and so is supported to the same extent as C11.

           gnu90
           gnu89
               GNU dialect of ISO C90 (including some C99 features).

           gnu99
           gnu9x
               GNU dialect of ISO C99.  The name gnu9x is deprecated.

           gnu11
           gnu1x
               GNU dialect of ISO C11.  The name gnu1x is deprecated.

           gnu17
           gnu18
               GNU dialect of ISO C17.  This is the default for C code.

           c++98
           c++03
               The 1998 ISO C++ standard plus the 2003 technical corrigendum and some additional defect reports. Same as -ansi for C++ code.

           gnu++98
           gnu++03
               GNU dialect of -std=c++98.

           c++11
           c++0x
               The 2011 ISO C++ standard plus amendments.  The name c++0x is deprecated.

           gnu++11
           gnu++0x
               GNU dialect of -std=c++11.  The name gnu++0x is deprecated.

           c++14
           c++1y
               The 2014 ISO C++ standard plus amendments.  The name c++1y is deprecated.

           gnu++14
           gnu++1y
               GNU dialect of -std=c++14.  This is the default for C++ code.  The name gnu++1y is deprecated.

           c++17
           c++1z
               The 2017 ISO C++ standard plus amendments.  The name c++1z is deprecated.
           gnu++17
           gnu++1z
               GNU dialect of -std=c++17.  The name gnu++1z is deprecated.

           c++2a
               The next revision of the ISO C++ standard, tentatively planned for 2020.  Support is highly experimental, and will almost certainly change in
               incompatible ways in future releases.

           gnu++2a
               GNU dialect of -std=c++2a.  Support is highly experimental, and will almost certainly change in incompatible ways in future releases.

In short: new GCC versions - as picked up by the new anaconda repo from @VictorOnink - redefine the standard C-version from C11 (GNU dialect) to C17 (GNU dialect), where hiding functions in macro's is prohibited.

[CKehl]

@VictorOnink - please check if the patch in #972 fixes your original problem

[VictorOnink]

I've installed the latest version of parcels and it seems to all work. I haven't run a full simulation but before it would crash when I would try to run from parcels import ParcelsRandom, and now that doesn't have any issues at all. So it looks good!