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Interface allowing R to use OpenCL
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Add missing headers when ocl.h doesn't include them #22

Open tom91136 opened 5 months ago

tom91136 commented 5 months ago

Some distro's OpenCL header (e.g AlmaLinux 9, also applies to any EL Linux like RHEL and Rocky) are conservative and does not transitively include stdlib.h so when building on such a platform, we get:

* installing to library ‘/root/tmp/libdir’
* installing *source* package ‘OpenCL’ ...
** package ‘OpenCL’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 11.4.1 20231218 (Red Hat 11.4.1-3)’
gcc -I"/root/r/dist/include" -DNDEBUG   -I/usr/local/include '-D_FORTIFY_SOURCE=2'  -fvisibility=hidden -fPIC  -g -O2 -Wall -pedantic -fexceptions -fstack-protector-strong -fstack-clash-protection -Werror=implicit-function-declaration -Wstrict-prototypes   -c buffer.c -o buffer.o
gcc -I"/root/r/dist/include" -DNDEBUG   -I/usr/local/include '-D_FORTIFY_SOURCE=2'  -fvisibility=hidden -fPIC  -g -O2 -Wall -pedantic -fexceptions -fstack-protector-strong -fstack-clash-protection -Werror=implicit-function-declaration -Wstrict-prototypes   -c ocl.c -o ocl.o
gcc -I"/root/r/dist/include" -DNDEBUG   -I/usr/local/include '-D_FORTIFY_SOURCE=2'  -fvisibility=hidden -fPIC  -g -O2 -Wall -pedantic -fexceptions -fstack-protector-strong -fstack-clash-protection -Werror=implicit-function-declaration -Wstrict-prototypes   -c oclerr.c -o oclerr.o
gcc -I"/root/r/dist/include" -DNDEBUG   -I/usr/local/include '-D_FORTIFY_SOURCE=2'  -fvisibility=hidden -fPIC  -g -O2 -Wall -pedantic -fexceptions -fstack-protector-strong -fstack-clash-protection -Werror=implicit-function-declaration -Wstrict-prototypes   -c reg.c -o reg.o
gcc -I"/root/r/dist/include" -DNDEBUG   -I/usr/local/include '-D_FORTIFY_SOURCE=2'  -fvisibility=hidden -fPIC  -g -O2 -Wall -pedantic -fexceptions -fstack-protector-strong -fstack-clash-protection -Werror=implicit-function-declaration -Wstrict-prototypes   -c wrap.c -o wrap.o
wrap.c: In function ‘R2size’:
wrap.c:143:23: error: implicit declaration of function ‘atoll’ [-Werror=implicit-function-declaration]
  143 |         long long l = atoll(c);
      |                       ^~~~~
buffer.c: In function ‘cl_read_buffer’:
buffer.c:197:32: error: implicit declaration of function ‘calloc’ [-Werror=implicit-function-declaration]
  197 |         intermediate = (float*)calloc(XLENGTH(res), sizeof(float));
      |                                ^~~~~~
buffer.c:7:1: note: include ‘<stdlib.h>’ or provide a declaration of ‘calloc’
    6 | #include <R_ext/Visibility.h>
  +++ |+#include <stdlib.h>
    7 | 
buffer.c:197:32: warning: incompatible implicit declaration of built-in function ‘calloc’ [-Wbuiltin-declaration-mismatch]
  197 |         intermediate = (float*)calloc(XLENGTH(res), sizeof(float));
      |                                ^~~~~~
buffer.c:197:32: note: include ‘<stdlib.h>’ or provide a declaration of ‘calloc’
buffer.c:206:13: error: implicit declaration of function ‘free’ [-Werror=implicit-function-declaration]
  206 |             free(intermediate);
      |             ^~~~
buffer.c:206:13: note: include ‘<stdlib.h>’ or provide a declaration of ‘free’
buffer.c:206:13: warning: incompatible implicit declaration of built-in function ‘free’ [-Wbuiltin-declaration-mismatch]
buffer.c:206:13: note: include ‘<stdlib.h>’ or provide a declaration of ‘free’
buffer.c:216:9: warning: incompatible implicit declaration of built-in function ‘free’ [-Wbuiltin-declaration-mismatch]
  216 |         free(intermediate);
      |         ^~~~
buffer.c:216:9: note: include ‘<stdlib.h>’ or provide a declaration of ‘free’
buffer.c: In function ‘cl_write_buffer’:
buffer.c:284:32: warning: incompatible implicit declaration of built-in function ‘calloc’ [-Wbuiltin-declaration-mismatch]
  284 |         intermediate = (float*)calloc(N, sizeof(float));
      |                                ^~~~~~
buffer.c:284:32: note: include ‘<stdlib.h>’ or provide a declaration of ‘calloc’
buffer.c:298:13: warning: incompatible implicit declaration of built-in function ‘free’ [-Wbuiltin-declaration-mismatch]
  298 |             free(intermediate);
      |             ^~~~
buffer.c:298:13: note: include ‘<stdlib.h>’ or provide a declaration of ‘free’
buffer.c:303:9: warning: incompatible implicit declaration of built-in function ‘free’ [-Wbuiltin-declaration-mismatch]
  303 |         free(intermediate);
      |         ^~~~
....  

While unverified, I suspect there is a high percentage of users with an NVIDIA OpenCL header which doesn't have this issue because the header is brought in at some point on their side.

This PR simply adds #include <stdlib.h> in the two places where's actually used. With this change, the package builds on vanilla AlmaLinux 9.4 with just ocl-icd-devel (OpenCL headers):

* installing to library ‘/root/tmp/libdir’
* installing *source* package ‘OpenCL’ ...
** using staged installation
files ‘src/buffer.c’, ‘src/wrap.c’ have the wrong MD5 checksums
** libs
using C compiler: ‘gcc (GCC) 11.4.1 20231218 (Red Hat 11.4.1-3)’
gcc -I"/root/r/dist/include" -DNDEBUG   -I/usr/local/include '-D_FORTIFY_SOURCE=2'  -fvisibility=hidden -fPIC  -g -O2 -Wall -pedantic -fexceptions -fstack-protector-strong -fstack-clash-protection -Werror=implicit-function-declaration -Wstrict-prototypes   -c wrap.c -o wrap.o
gcc -shared -L/root/r/dist/lib -L/usr/local/lib -o OpenCL.so buffer.o ocl.o oclerr.o reg.o wrap.o -lOpenCL -L/root/r/dist/lib -lR
mv OpenCL.so R_OpenCL.so
installing to /root/tmp/libdir/00LOCK-OpenCL/00new/OpenCL/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (OpenCL)