Hi,
Here you go:
cmake .. -DCMAKE_INSTALL_PREFIX=/appl/openbabel-3.0.0
-DEIGEN3_INCLUDE_DIR=/appl/eigen-3.3.4/include
-DBOOST_ROOT=/appl/boost-1.65.1/include -DCMAKE_BUILD_TYPE=DEBUG -DRUN_SWIG=ON
-- The C compiler identification is GNU 4.9.4
-- The CXX compiler identification is GNU 4.9.4
-- Check for working C compiler: /appl/gcc-4.9.4/bin/cc
-- Check for working C compiler: /appl/gcc-4.9.4/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /appl/gcc-4.9.4/bin/c++
-- Check for working CXX compiler: /appl/gcc-4.9.4/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Deprecation Warning at CMakeLists.txt:12 (cmake_policy):
The OLD behavior for policy CMP0042 will be removed from a future version
of CMake.
The cmake-policies(7) manual explains that the OLD behaviors of all
policies are deprecated and that a policy should be set to OLD only under
specific short-term circumstances. Projects should be ported to the NEW
behavior and not rely on setting a policy to OLD.
-- Performing Test COMPILER_SUPPORTS_CXX11
-- Performing Test COMPILER_SUPPORTS_CXX11 - Success
-- Performing Test COMPILER_SUPPORTS_CXX0X
-- Performing Test COMPILER_SUPPORTS_CXX0X - Success
-- Using included inchi library.
-- Found LibXml2: /usr/lib64/libxml2.so (found version "2.9.1")
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.7")
-- Found wxWidgets:
-L/appl/wxwidgets-3.1.3/lib;-pthread;;;-lwx_baseu-3.1;-lwx_x11univu_core-3.1
(found version "3.1.3")
-- Looking for conio.h
-- Looking for conio.h - not found
-- Looking for sys/time.h
-- Looking for sys/time.h - found
-- Looking for time.h
-- Looking for time.h - found
-- Looking for strings.h
-- Looking for strings.h - found
-- Looking for rpc/xdr.h
-- Looking for rpc/xdr.h - found
-- Looking for regex.h
-- Looking for regex.h - found
-- Looking for C++ include sstream
-- Looking for C++ include sstream - found
-- Looking for rint
-- Looking for rint - not found
-- Looking for snprintf
-- Looking for snprintf - found
-- Looking for sranddev
-- Looking for sranddev - not found
-- Looking for strcasecmp
-- Looking for strcasecmp - found
-- Looking for strncasecmp
-- Looking for strncasecmp - found
-- Looking for dlopen in dl
-- Looking for dlopen in dl - found
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of clock_t
-- Check size of clock_t - done
-- Performing Test SCANDIR_NEEDS_CONST
-- Performing Test SCANDIR_NEEDS_CONST - Failed
-- Performing Test HAVE_GCC_VISIBILITY
-- Performing Test HAVE_GCC_VISIBILITY - Success
-- Checking available shared pointer...
-- Performing Test HAVE_STD_SHARED_PTR
-- Performing Test HAVE_STD_SHARED_PTR - Success
-- Performing Test HAVE_STD_TR1_SHARED_PTR
-- Performing Test HAVE_STD_TR1_SHARED_PTR - Failed
-- Performing Test HAVE_STD_TR1_SHARED_PTR_IN_TR1_HEADER
-- Performing Test HAVE_STD_TR1_SHARED_PTR_IN_TR1_HEADER - Success
-- Use std::shared_ptr in memory
-- Boost version: 1.65.1
-- Found the following Boost libraries:
-- program_options
-- iostreams
-- regex
CMake Error at cmake/modules/FindEigen3.cmake:33 (file):
file failed to open for reading (No such file or directory):
/appl/eigen-3.3.4/include/Eigen/src/Core/util/Macros.h
Call Stack (most recent call first):
cmake/modules/FindEigen3.cmake:59 (_eigen3_check_version)
CMakeLists.txt:467 (find_package)
-- Could NOT find Eigen2 (missing: EIGEN2_INCLUDE_DIR EIGEN2_VERSION_OK)
(Required is at least version "2.0.0")
-- Boost version: 1.65.1
-- Boost version: 1.65.1
-- Found the following Boost libraries:
-- iostreams
-- unit_test_framework
-- regex
-- Maestro formats will be supported. Using MaeParser 1.1 at
-- Found PkgConfig: /bin/pkg-config (found version "0.27.1")
-- Could NOT find RapidJSON (missing: RAPIDJSON_INCLUDE_DIRS) (Required is at
least version "1.1.0")
-- JSON formats will be supported. Using RapidJSON 1.1.0 at
/appl/src/openbabel-openbabel-3-0-0/external/rapidjson-1.1.0/include
-- Checking for module 'cairo'
-- Found cairo, version 1.15.12
-- Found Cairo: /usr/lib64/libcairo.so
-- Cairo found. PNG output will be supported.
-- Boost version: 1.65.1
-- Found the following Boost libraries:
-- system
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Boost version: 1.65.1
-- Found the following Boost libraries:
-- program_options
-- iostreams
-- regex
-- Looking for getopt
-- Looking for getopt - found
-- Attempting to build the GUI
-- wxWidgets found => GUI will be built
-- Found PythonInterp: /appl/python-2.7.14/bin/python (found version "2.7.14")
-- Could NOT find SWIG (missing: SWIG_EXECUTABLE SWIG_DIR)
-- Could NOT find SWIG (missing: SWIG_EXECUTABLE SWIG_DIR) (Required is at
least version "2.0")
-- SWIG 2.0 NOT found
-- Configuring incomplete, errors occurred!
See also "/appl/src/openbabel-openbabel-3-0-0/build/CMakeFiles/CMakeOutput.log".
See also "/appl/src/openbabel-openbabel-3-0-0/build/CMakeFiles/CMakeError.log".
[root@revan build]# cd ..
[root@revan openbabel-openbabel-3-0-0]# rm -rf build
[root@revan openbabel-openbabel-3-0-0]# mkdir build
[root@revan openbabel-openbabel-3-0-0]# module load swig
[root@revan openbabel-openbabel-3-0-0]# cd build
[root@revan build]# cmake .. -DCMAKE_INSTALL_PREFIX=/appl/openbabel-3.0.0
-DEIGEN3_INCLUDE_DIR=/appl/eigen-3.3.4/include
-DBOOST_ROOT=/appl/boost-1.65.1/include -DCMAKE_BUILD_TYPE=DEBUG -DRUN_SWIG=ON
-- The C compiler identification is GNU 4.9.4
-- The CXX compiler identification is GNU 4.9.4
-- Check for working C compiler: /appl/gcc-4.9.4/bin/cc
-- Check for working C compiler: /appl/gcc-4.9.4/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /appl/gcc-4.9.4/bin/c++
-- Check for working CXX compiler: /appl/gcc-4.9.4/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Deprecation Warning at CMakeLists.txt:12 (cmake_policy):
The OLD behavior for policy CMP0042 will be removed from a future version
of CMake.
The cmake-policies(7) manual explains that the OLD behaviors of all
policies are deprecated and that a policy should be set to OLD only under
specific short-term circumstances. Projects should be ported to the NEW
behavior and not rely on setting a policy to OLD.
-- Performing Test COMPILER_SUPPORTS_CXX11
-- Performing Test COMPILER_SUPPORTS_CXX11 - Success
-- Performing Test COMPILER_SUPPORTS_CXX0X
-- Performing Test COMPILER_SUPPORTS_CXX0X - Success
-- Using included inchi library.
-- Found LibXml2: /usr/lib64/libxml2.so (found version "2.9.1")
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.7")
-- Found wxWidgets:
-L/appl/wxwidgets-3.1.3/lib;-pthread;;;-lwx_baseu-3.1;-lwx_x11univu_core-3.1
(found version "3.1.3")
-- Looking for conio.h
-- Looking for conio.h - not found
-- Looking for sys/time.h
-- Looking for sys/time.h - found
-- Looking for time.h
-- Looking for time.h - found
-- Looking for strings.h
-- Looking for strings.h - found
-- Looking for rpc/xdr.h
-- Looking for rpc/xdr.h - found
-- Looking for regex.h
-- Looking for regex.h - found
-- Looking for C++ include sstream
-- Looking for C++ include sstream - found
-- Looking for rint
-- Looking for rint - not found
-- Looking for snprintf
-- Looking for snprintf - found
-- Looking for sranddev
-- Looking for sranddev - not found
-- Looking for strcasecmp
-- Looking for strcasecmp - found
-- Looking for strncasecmp
-- Looking for strncasecmp - found
-- Looking for dlopen in dl
-- Looking for dlopen in dl - found
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of clock_t
-- Check size of clock_t - done
-- Performing Test SCANDIR_NEEDS_CONST
-- Performing Test SCANDIR_NEEDS_CONST - Failed
-- Performing Test HAVE_GCC_VISIBILITY
-- Performing Test HAVE_GCC_VISIBILITY - Success
-- Checking available shared pointer...
-- Performing Test HAVE_STD_SHARED_PTR
-- Performing Test HAVE_STD_SHARED_PTR - Success
-- Performing Test HAVE_STD_TR1_SHARED_PTR
-- Performing Test HAVE_STD_TR1_SHARED_PTR - Failed
-- Performing Test HAVE_STD_TR1_SHARED_PTR_IN_TR1_HEADER
-- Performing Test HAVE_STD_TR1_SHARED_PTR_IN_TR1_HEADER - Success
-- Use std::shared_ptr in memory
-- Boost version: 1.65.1
-- Found the following Boost libraries:
-- program_options
-- iostreams
-- regex
CMake Error at cmake/modules/FindEigen3.cmake:33 (file):
file failed to open for reading (No such file or directory):
/appl/eigen-3.3.4/include/Eigen/src/Core/util/Macros.h
Call Stack (most recent call first):
cmake/modules/FindEigen3.cmake:59 (_eigen3_check_version)
CMakeLists.txt:467 (find_package)
-- Could NOT find Eigen2 (missing: EIGEN2_INCLUDE_DIR EIGEN2_VERSION_OK)
(Required is at least version "2.0.0")
-- Boost version: 1.65.1
-- Boost version: 1.65.1
-- Found the following Boost libraries:
-- iostreams
-- unit_test_framework
-- regex
-- Maestro formats will be supported. Using MaeParser 1.1 at
-- Found PkgConfig: /bin/pkg-config (found version "0.27.1")
-- Could NOT find RapidJSON (missing: RAPIDJSON_INCLUDE_DIRS) (Required is at
least version "1.1.0")
-- JSON formats will be supported. Using RapidJSON 1.1.0 at
/appl/src/openbabel-openbabel-3-0-0/external/rapidjson-1.1.0/include
-- Checking for module 'cairo'
-- Found cairo, version 1.15.12
-- Found Cairo: /usr/lib64/libcairo.so
-- Cairo found. PNG output will be supported.
-- Boost version: 1.65.1
-- Found the following Boost libraries:
-- system
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Boost version: 1.65.1
-- Found the following Boost libraries:
-- program_options
-- iostreams
-- regex
-- Looking for getopt
-- Looking for getopt - found
-- Attempting to build the GUI
-- wxWidgets found => GUI will be built
-- Found PythonInterp: /appl/python-2.7.14/bin/python (found version "2.7.14")
-- Found SWIG: /appl/swig-4.0.1/bin/swig (found version "4.0.1")
-- Found SWIG: /appl/swig-4.0.1/bin/swig (found suitable version "4.0.1",
minimum required is "2.0")
-- Configuring incomplete, errors occurred!
See also "/appl/src/openbabel-openbabel-3-0-0/build/CMakeFiles/CMakeOutput.log".
See also "/appl/src/openbabel-openbabel-3-0-0/build/CMakeFiles/CMakeError.log".
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/
________________________________________
From: Noel O'Boyle <baoille...@gmail.com>
Sent: Thursday, April 23, 2020 3:04 AM
To: Weise, David
Cc: openbabel-discuss@lists.sourceforge.net
Subject: Re: [Open Babel] cmake problems
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<mailto: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
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--David Weise
David Weise
Linux Systems Admin
Penn Medicine Academic Computing Services (PMACS)
Richards Medical Labs
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http://www.med.upenn.edu/pmacs/
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