Hi David,
Can you provide the output from running Cmake on a clean build of Open
Babel 3.0? What exact OS is this?
- Noel
On Wed, 22 Apr 2020, 19:17 Weise, David, <dwe...@upenn.edu> wrote:
> Hello Everybody,
> I've been trying to compile openbabel for a hpc lsf environment. I'm
> having a problem with cmake and ld. It can't find -pthreads. Can someone
> shed some light on this? The error is below:
> Determining if the include file conio.h exists failed with the following
> output:
> Change Dir: /appl/src/openbabel-openbabel-3-0-0/build/CMakeFiles/CMakeTmp
>
> Run Build Command(s):/bin/gmake cmTC_126b6/fast
> /bin/gmake -f CMakeFiles/cmTC_126b6.dir/build.make
> CMakeFiles/cmTC_126b6.dir/build
> gmake[1]: Entering directory
> `/misc/appl/src/openbabel-openbabel-3-0-0/build/CMakeFiles/CMakeTmp'
> Building C object CMakeFiles/cmTC_126b6.dir/CheckIncludeFile.c.o
> /appl/gcc-4.9.4/bin/cc -fPIE -o
> CMakeFiles/cmTC_126b6.dir/CheckIncludeFile.c.o -c
> /appl/src/openbabel-openbabel-3-0-0/build/CMakeFiles/CMakeTmp/CheckIncludeFile.c
> /appl/src/openbabel-openbabel-3-0-0/build/CMakeFiles/CMakeTmp/CheckIncludeFile.c:1:19:
> fatal error: conio.h: No such file or directory
> #include <conio.h>
> ^
> compilation terminated.
> gmake[1]: *** [CMakeFiles/cmTC_126b6.dir/CheckIncludeFile.c.o] Error 1
> gmake[1]: Leaving directory
> `/misc/appl/src/openbabel-openbabel-3-0-0/build/CMakeFiles/CMakeTmp'
> gmake: *** [cmTC_126b6/fast] Error 2
>
>
> Determining if the rint exist failed with the following output:
> Change Dir: /appl/src/openbabel-openbabel-3-0-0/build/CMakeFiles/CMakeTmp
>
> Run Build Command(s):/bin/gmake cmTC_71986/fast
> /bin/gmake -f CMakeFiles/cmTC_71986.dir/build.make
> CMakeFiles/cmTC_71986.dir/build
> gmake[1]: Entering directory
> `/misc/appl/src/openbabel-openbabel-3-0-0/build/CMakeFiles/CMakeTmp'
> Building C object CMakeFiles/cmTC_71986.dir/CheckSymbolExists.c.o
> /appl/gcc-4.9.4/bin/cc -fPIE -o
> CMakeFiles/cmTC_71986.dir/CheckSymbolExists.c.o -c
> /appl/src/openbabel-openbabel-3-0-0/build/CMakeFiles/CMakeTmp/CheckSymbolExists.c
> Linking C executable cmTC_71986
> /appl/cmake-3.14.5/bin/cmake -E cmake_link_script
> CMakeFiles/cmTC_71986.dir/link.txt --verbose=1
> /appl/gcc-4.9.4/bin/cc -rdynamic
> CMakeFiles/cmTC_71986.dir/CheckSymbolExists.c.o -o cmTC_71986
> CMakeFiles/cmTC_71986.dir/CheckSymbolExists.c.o: In function `main':
> CheckSymbolExists.c:(.text+0x1b): undefined reference to `rint'
> collect2: error: ld returned 1 exit status
> gmake[1]: *** [cmTC_71986] Error 1
> gmake[1]: Leaving directory
> `/misc/appl/src/openbabel-openbabel-3-0-0/build/CMakeFiles/CMakeTmp'
> gmake: *** [cmTC_71986/fast] Error 2
>
> File
> /appl/src/openbabel-openbabel-3-0-0/build/CMakeFiles/CMakeTmp/CheckSymbolExists.c:
> /* */
> #include <math.h>
>
> int main(int argc, char** argv)
> {
> (void)argv;
> #ifndef rint
> return ((int*)(&rint))[argc];
> #else
> (void)argc;
> return 0;
> #endif
> }
>
> Determining if the sranddev exist failed with the following output:
> Change Dir: /appl/src/openbabel-openbabel-3-0-0/build/CMakeFiles/CMakeTmp
>
> Run Build Command(s):/bin/gmake cmTC_c4a93/fast
> /bin/gmake -f CMakeFiles/cmTC_c4a93.dir/build.make
> CMakeFiles/cmTC_c4a93.dir/build
> gmake[1]: Entering directory
> `/misc/appl/src/openbabel-openbabel-3-0-0/build/CMakeFiles/CMakeTmp'
> Building C object CMakeFiles/cmTC_c4a93.dir/CheckSymbolExists.c.o
> /appl/gcc-4.9.4/bin/cc -fPIE -o
> CMakeFiles/cmTC_c4a93.dir/CheckSymbolExists.c.o -c
> /appl/src/openbabel-openbabel-3-0-0/build/CMakeFiles/CMakeTmp/CheckSymbolExists.c
> /appl/src/openbabel-openbabel-3-0-0/build/CMakeFiles/CMakeTmp/CheckSymbolExists.c:
> In function ‘main’:
> /appl/src/openbabel-openbabel-3-0-0/build/CMakeFiles/CMakeTmp/CheckSymbolExists.c:8:19:
> error: ‘sranddev’ undeclared (first use in this function)
> return ((int*)(&sranddev))[argc];
> ^
> /appl/src/openbabel-openbabel-3-0-0/build/CMakeFiles/CMakeTmp/CheckSymbolExists.c:8:19:
> note: each undeclared identifier is reported only once for each function it
> appears in
> gmake[1]: *** [CMakeFiles/cmTC_c4a93.dir/CheckSymbolExists.c.o] Error 1
> gmake[1]: Leaving directory
> `/misc/appl/src/openbabel-openbabel-3-0-0/build/CMakeFiles/CMakeTmp'
> gmake: *** [cmTC_c4a93/fast] Error 2
>
> File
> /appl/src/openbabel-openbabel-3-0-0/build/CMakeFiles/CMakeTmp/CheckSymbolExists.c:
> /* */
> #include <stdlib.h>
>
> int main(int argc, char** argv)
> {
> (void)argv;
> #ifndef sranddev
> return ((int*)(&sranddev))[argc];
> #else
> (void)argc;
> return 0;
> #endif
> }
>
> Performing C SOURCE FILE Test SCANDIR_NEEDS_CONST failed with the
> following output:
> Change Dir: /appl/src/openbabel-openbabel-3-0-0/build/CMakeFiles/CMakeTmp
>
> Run Build Command(s):/bin/gmake cmTC_9679c/fast
> /bin/gmake -f CMakeFiles/cmTC_9679c.dir/build.make
> CMakeFiles/cmTC_9679c.dir/build
> gmake[1]: Entering directory
> `/misc/appl/src/openbabel-openbabel-3-0-0/build/CMakeFiles/CMakeTmp'
> Building C object CMakeFiles/cmTC_9679c.dir/src.c.o
> /appl/gcc-4.9.4/bin/cc -DSCANDIR_NEEDS_CONST -Werror -fPIE -o
> CMakeFiles/cmTC_9679c.dir/src.c.o -c
> /appl/src/openbabel-openbabel-3-0-0/build/CMakeFiles/CMakeTmp/src.c
> /appl/src/openbabel-openbabel-3-0-0/build/CMakeFiles/CMakeTmp/src.c: In
> function ‘main’:
> /appl/src/openbabel-openbabel-3-0-0/build/CMakeFiles/CMakeTmp/src.c:7:46:
> error: passing argument 3 of ‘scandir’ from incompatible pointer type
> [-Werror]
> int count = scandir ("./", &entries_pp, matchFiles, 0);
> ^
> In file included from
> /appl/src/openbabel-openbabel-3-0-0/build/CMakeFiles/CMakeTmp/src.c:3:0:
> /usr/include/dirent.h:255:12: note: expected ‘int (*)(const struct dirent
> *)’ but argument is of type ‘int (*)(struct dirent *)’
> extern int scandir (const char *__restrict __dir,
> ^
> cc1: all warnings being treated as errors
> gmake[1]: *** [CMakeFiles/cmTC_9679c.dir/src.c.o] Error 1
> gmake[1]: Leaving directory
> `/misc/appl/src/openbabel-openbabel-3-0-0/build/CMakeFiles/CMakeTmp'
> gmake: *** [cmTC_9679c/fast] Error 2
>
> Source file was:
>
> #include <sys/types.h>
> #include <dirent.h>
> int main(){
> extern int matchFiles (struct dirent *entry_p);
> struct dirent **entries_pp;
> int count = scandir ("./", &entries_pp, matchFiles, 0);
> return count;
> }
>
> Performing C++ SOURCE FILE Test HAVE_STD_TR1_SHARED_PTR failed with the
> following output:
> Change Dir: /appl/src/openbabel-openbabel-3-0-0/build/CMakeFiles/CMakeTmp
>
> Run Build Command(s):/bin/gmake cmTC_d9e1e/fast
> /bin/gmake -f CMakeFiles/cmTC_d9e1e.dir/build.make
> CMakeFiles/cmTC_d9e1e.dir/build
> gmake[1]: Entering directory
> `/misc/appl/src/openbabel-openbabel-3-0-0/build/CMakeFiles/CMakeTmp'
> Building CXX object CMakeFiles/cmTC_d9e1e.dir/src.cxx.o
> /appl/gcc-4.9.4/bin/c++ -std=c++11 -pthread -DHAVE_STD_TR1_SHARED_PTR
> -Werror -fPIE -o CMakeFiles/cmTC_d9e1e.dir/src.cxx.o -c
> /appl/src/openbabel-openbabel-3-0-0/build/CMakeFiles/CMakeTmp/src.cxx
> /appl/src/openbabel-openbabel-3-0-0/build/CMakeFiles/CMakeTmp/src.cxx: In
> function ‘int main()’:
> /appl/src/openbabel-openbabel-3-0-0/build/CMakeFiles/CMakeTmp/src.cxx:2:45:
> error: ‘std::tr1’ has not been declared
> int main(){ std::tr1::shared_ptr<int> p;
> return 0; }
> ^
> /appl/src/openbabel-openbabel-3-0-0/build/CMakeFiles/CMakeTmp/src.cxx:2:61:
> error: expected primary-expression before ‘int’
> int main(){ std::tr1::shared_ptr<int> p;
> return 0; }
> ^
> gmake[1]: *** [CMakeFiles/cmTC_d9e1e.dir/src.cxx.o] Error 1
> gmake[1]: Leaving directory
> `/misc/appl/src/openbabel-openbabel-3-0-0/build/CMakeFiles/CMakeTmp'
> gmake: *** [cmTC_d9e1e/fast] Error 2
>
> Source file was:
> #include <memory>
> int main(){ std::tr1::shared_ptr<int> p; return
> 0; }
> Determining if the pthread_create exist failed with the following output:
> Change Dir: /appl/src/openbabel-openbabel-3-0-0/build/CMakeFiles/CMakeTmp
>
> Run Build Command(s):/bin/gmake cmTC_26311/fast
> /bin/gmake -f CMakeFiles/cmTC_26311.dir/build.make
> CMakeFiles/cmTC_26311.dir/build
> gmake[1]: Entering directory
> `/misc/appl/src/openbabel-openbabel-3-0-0/build/CMakeFiles/CMakeTmp'
> Building C object CMakeFiles/cmTC_26311.dir/CheckSymbolExists.c.o
> /appl/gcc-4.9.4/bin/cc -Werror -fPIE -o
> CMakeFiles/cmTC_26311.dir/CheckSymbolExists.c.o -c
> /appl/src/openbabel-openbabel-3-0-0/build/CMakeFiles/CMakeTmp/CheckSymbolExists.c
> Linking C executable cmTC_26311
> /appl/cmake-3.14.5/bin/cmake -E cmake_link_script
> CMakeFiles/cmTC_26311.dir/link.txt --verbose=1
> /appl/gcc-4.9.4/bin/cc -Werror -rdynamic
> CMakeFiles/cmTC_26311.dir/CheckSymbolExists.c.o -o cmTC_26311
> CMakeFiles/cmTC_26311.dir/CheckSymbolExists.c.o: In function `main':
> CheckSymbolExists.c:(.text+0x1b): undefined reference to `pthread_create'
> collect2: error: ld returned 1 exit status
> gmake[1]: *** [cmTC_26311] Error 1
> gmake[1]: Leaving directory
> `/misc/appl/src/openbabel-openbabel-3-0-0/build/CMakeFiles/CMakeTmp'
> gmake: *** [cmTC_26311/fast] Error 2
>
> File
> /appl/src/openbabel-openbabel-3-0-0/build/CMakeFiles/CMakeTmp/CheckSymbolExists.c:
> /* */
> #include <pthread.h>
>
> int main(int argc, char** argv)
> {
> (void)argv;
> #ifndef pthread_create
> return ((int*)(&pthread_create))[argc];
> #else
> (void)argc;
> return 0;
> #endif
> }
>
> Determining if the function pthread_create exists in the pthreads failed
> with the following output:
> Change Dir: /appl/src/openbabel-openbabel-3-0-0/build/CMakeFiles/CMakeTmp
>
> Run Build Command(s):/bin/gmake cmTC_56164/fast
> /bin/gmake -f CMakeFiles/cmTC_56164.dir/build.make
> CMakeFiles/cmTC_56164.dir/build
> gmake[1]: Entering directory
> `/misc/appl/src/openbabel-openbabel-3-0-0/build/CMakeFiles/CMakeTmp'
> Building C object CMakeFiles/cmTC_56164.dir/CheckFunctionExists.c.o
> /appl/gcc-4.9.4/bin/cc -DCHECK_FUNCTION_EXISTS=pthread_create -Werror
> -fPIE -o CMakeFiles/cmTC_56164.dir/CheckFunctionExists.c.o -c
> /appl/cmake-3.14.5/share/cmake-3.14/Modules/CheckFunctionExists.c
> Linking C executable cmTC_56164
> /appl/cmake-3.14.5/bin/cmake -E cmake_link_script
> CMakeFiles/cmTC_56164.dir/link.txt --verbose=1
> /appl/gcc-4.9.4/bin/cc -DCHECK_FUNCTION_EXISTS=pthread_create -Werror
> -rdynamic CMakeFiles/cmTC_56164.dir/CheckFunctionExists.c.o -o cmTC_56164
> -lpthreads
> /bin/ld: cannot find -lpthreads
> collect2: error: ld returned 1 exit status
> gmake[1]: *** [cmTC_56164] Error 1
> gmake[1]: Leaving directory
> `/misc/appl/src/openbabel-openbabel-3-0-0/build/CMakeFiles/CMakeTmp'
> gmake: *** [cmTC_56164/fast] Error 2
>
>
> --David Weise
>
>
>
> David Weise
> Linux Systems Admin
> Penn Medicine Academic Computing Services (PMACS)
> Richards Medical Labs
> 3700 Hamilton Walk | Philadelphia, PA 19104
> http://www.med.upenn.edu/pmacs/
>
>
>
> _______________________________________________
> OpenBabel-discuss mailing list
> OpenBabel-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>
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