Compiling error

[Shicai Wang]

Hi,

I tried to re-compile to test my examples but got some error.

My system config:

Ubuntu 14.04

gcc (Ubuntu 4.8.2-19ubuntu1) 4.8.2

cmake version 2.8.12.2

java version "1.7.0_65"
OpenJDK Runtime Environment (IcedTea 2.5.3) (7u71-2.5.3-0ubuntu0.14.04.1)
OpenJDK 64-Bit Server VM (build 24.65-b04, mixed mode)

datampi-0.6.0

MPICH2


Console output:

mpiuser@rmpi02:~/datampi-0.6.0-build$ cmake -D CMAKE_INSTALL_PREFIX=/home/mpiuser/datampi-0.6.0-install     -D MPI_D_BUILD_DOCS=OFF -D MPI_D_BUILD_TESTS=OFF -D MPI_D_BUILD_EXAMPLES=OFF     -D MPI_D_BUILD_BENCHMARKS=ON /home/mpiuser/datampi-0.6.0-src
-- Java version 1.7.0.65 configured successfully!
-- Could NOT find JNI (missing:  JAVA_AWT_LIBRARY JAVA_JVM_LIBRARY JAVA_INCLUDE_PATH JAVA_INCLUDE_PATH2 JAVA_AWT_INCLUDE_PATH)
-- Check if compiler accepts -pthread
-- Check if compiler accepts -pthread - yes
CMake Error: The following variables are used in this project, but they are set to NOTFOUND.
Please set them or make sure they are set and tested correctly in the CMake files:
JAVA_INCLUDE_PATH (ADVANCED)
   used as include directory in directory /home/mpiuser/datampi-0.6.0-src/src/C
   used as include directory in directory /home/mpiuser/datampi-0.6.0-src/src/C
   used as include directory in directory /home/mpiuser/datampi-0.6.0-src/src/bin
   used as include directory in directory /home/mpiuser/datampi-0.6.0-src/src/bin
JAVA_INCLUDE_PATH2 (ADVANCED)
   used as include directory in directory /home/mpiuser/datampi-0.6.0-src/src/C
   used as include directory in directory /home/mpiuser/datampi-0.6.0-src/src/C
   used as include directory in directory /home/mpiuser/datampi-0.6.0-src/src/bin
   used as include directory in directory /home/mpiuser/datampi-0.6.0-src/src/bin

-- Configuring incomplete, errors occurred!
See also "/home/mpiuser/datampi-0.6.0-build/CMakeFiles/CMakeOutput.log".
See also "/home/mpiuser/datampi-0.6.0-build/CMakeFiles/CMakeError.log".

CMakeOutput.log

The system is: Linux - 3.13.0-24-generic - x86_64
Compiling the C compiler identification source file "CMakeCCompilerId.c" succeeded.
Compiler: /usr/bin/cc
Build flags:
Id flags:

The output was:
0


Compilation of the C compiler identification source "CMakeCCompilerId.c" produced "a.out"

The C compiler identification is GNU, found in "/home/mpiuser/datampi-0.6.0-build/CMakeFiles/2.8.12.2/CompilerIdC/a.out"

Determining if the C compiler works passed with the following output:
Change Dir: /home/mpiuser/datampi-0.6.0-build/CMakeFiles/CMakeTmp

Run Build Command:/usr/bin/make "cmTryCompileExec1730127296/fast"
/usr/bin/make -f CMakeFiles/cmTryCompileExec1730127296.dir/build.make CMakeFiles/cmTryCompileExec1730127296.dir/build
make[1]: Entering directory `/home/mpiuser/datampi-0.6.0-build/CMakeFiles/CMakeTmp'
/usr/bin/cmake -E cmake_progress_report /home/mpiuser/datampi-0.6.0-build/CMakeFiles/CMakeTmp/CMakeFiles 1
Building C object CMakeFiles/cmTryCompileExec1730127296.dir/testCCompiler.c.o
/usr/bin/cc    -o CMakeFiles/cmTryCompileExec1730127296.dir/testCCompiler.c.o   -c /home/mpiuser/datampi-0.6.0-build/CMakeFiles/CMakeTmp/testCCompiler.c
Linking C executable cmTryCompileExec1730127296
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec1730127296.dir/link.txt --verbose=1
/usr/bin/cc       CMakeFiles/cmTryCompileExec1730127296.dir/testCCompiler.c.o  -o cmTryCompileExec1730127296 -rdynamic
make[1]: Leaving directory `/home/mpiuser/datampi-0.6.0-build/CMakeFiles/CMakeTmp'


Detecting C compiler ABI info compiled with the following output:
Change Dir: /home/mpiuser/datampi-0.6.0-build/CMakeFiles/CMakeTmp

Run Build Command:/usr/bin/make "cmTryCompileExec1770851417/fast"
/usr/bin/make -f CMakeFiles/cmTryCompileExec1770851417.dir/build.make CMakeFiles/cmTryCompileExec1770851417.dir/build
make[1]: Entering directory `/home/mpiuser/datampi-0.6.0-build/CMakeFiles/CMakeTmp'
/usr/bin/cmake -E cmake_progress_report /home/mpiuser/datampi-0.6.0-build/CMakeFiles/CMakeTmp/CMakeFiles 1
Building C object CMakeFiles/cmTryCompileExec1770851417.dir/CMakeCCompilerABI.c.o
/usr/bin/cc    -o CMakeFiles/cmTryCompileExec1770851417.dir/CMakeCCompilerABI.c.o   -c /usr/share/cmake-2.8/Modules/CMakeCCompilerABI.c
Linking C executable cmTryCompileExec1770851417
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec1770851417.dir/link.txt --verbose=1
/usr/bin/cc     -v CMakeFiles/cmTryCompileExec1770851417.dir/CMakeCCompilerABI.c.o  -o cmTryCompileExec1770851417 -rdynamic 
Using built-in specs.
COLLECT_GCC=/usr/bin/cc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/4.8/lto-wrapper
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 4.8.2-19ubuntu1' --with-bugurl=file:///usr/share/doc/gcc-4.8/README.Bugs --enable-languages=c,c++,java,go,d,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-4.8 --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.8 --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-gnu-unique-object --disable-libmudflap --enable-plugin --with-system-zlib --disable-browser-plugin --enable-java-awt=gtk --enable-gtk-cairo --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-4.8-amd64/jre --enable-java-home --with-jvm-root-dir=/usr/lib/jvm/java-1.5.0-gcj-4.8-amd64 --with-jvm-jar-dir=/usr/lib/jvm-exports/java-1.5.0-gcj-4.8-amd64 --with-arch-directory=amd64 --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --enable-objc-gc --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 4.8.2 (Ubuntu 4.8.2-19ubuntu1)
COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/4.8/:/usr/lib/gcc/x86_64-linux-gnu/4.8/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/4.8/:/usr/lib/gcc/x86_64-linux-gnu/
LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/4.8/:/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../:/lib/:/usr/lib/
COLLECT_GCC_OPTIONS='-v' '-o' 'cmTryCompileExec1770851417' '-rdynamic' '-mtune=generic' '-march=x86-64'
 /usr/lib/gcc/x86_64-linux-gnu/4.8/collect2 --sysroot=/ --build-id --eh-frame-hdr -m elf_x86_64 --hash-style=gnu --as-needed -export-dynamic -dynamic-linker /lib64/ld-linux-x86-64.so.2 -z relro -o cmTryCompileExec1770851417 /usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu/crt1.o /usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/4.8/crtbegin.o -L/usr/lib/gcc/x86_64-linux-gnu/4.8 -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/4.8/../../.. CMakeFiles/cmTryCompileExec1770851417.dir/CMakeCCompilerABI.c.o -lgcc --as-needed -lgcc_s --no-as-needed -lc -lgcc --as-needed -lgcc_s --no-as-needed /usr/lib/gcc/x86_64-linux-gnu/4.8/crtend.o /usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu/crtn.o
make[1]: Leaving directory `/home/mpiuser/datampi-0.6.0-build/CMakeFiles/CMakeTmp'


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Determining if files pthread.h exist passed with the following output:
Change Dir: /home/mpiuser/datampi-0.6.0-build/CMakeFiles/CMakeTmp

Run Build Command:/usr/bin/make "cmTryCompileExec3745185423/fast"
/usr/bin/make -f CMakeFiles/cmTryCompileExec3745185423.dir/build.make CMakeFiles/cmTryCompileExec3745185423.dir/build
make[1]: Entering directory `/home/mpiuser/datampi-0.6.0-build/CMakeFiles/CMakeTmp'
/usr/bin/cmake -E cmake_progress_report /home/mpiuser/datampi-0.6.0-build/CMakeFiles/CMakeTmp/CMakeFiles 1
Building C object CMakeFiles/cmTryCompileExec3745185423.dir/CheckIncludeFiles.c.o
/usr/bin/cc    -o CMakeFiles/cmTryCompileExec3745185423.dir/CheckIncludeFiles.c.o   -c /home/mpiuser/datampi-0.6.0-build/CMakeFiles/CMakeTmp/CheckIncludeFiles.c
Linking C executable cmTryCompileExec3745185423
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec3745185423.dir/link.txt --verbose=1
/usr/bin/cc       CMakeFiles/cmTryCompileExec3745185423.dir/CheckIncludeFiles.c.o  -o cmTryCompileExec3745185423 -rdynamic
make[1]: Leaving directory `/home/mpiuser/datampi-0.6.0-build/CMakeFiles/CMakeTmp'


Determining if the function pthread_create exists in the pthread passed with the following output:
Change Dir: /home/mpiuser/datampi-0.6.0-build/CMakeFiles/CMakeTmp

Run Build Command:/usr/bin/make "cmTryCompileExec2090637266/fast"
/usr/bin/make -f CMakeFiles/cmTryCompileExec2090637266.dir/build.make CMakeFiles/cmTryCompileExec2090637266.dir/build
make[1]: Entering directory `/home/mpiuser/datampi-0.6.0-build/CMakeFiles/CMakeTmp'
/usr/bin/cmake -E cmake_progress_report /home/mpiuser/datampi-0.6.0-build/CMakeFiles/CMakeTmp/CMakeFiles 1
Building C object CMakeFiles/cmTryCompileExec2090637266.dir/CheckFunctionExists.c.o
/usr/bin/cc   -DCHECK_FUNCTION_EXISTS=pthread_create   -o CMakeFiles/cmTryCompileExec2090637266.dir/CheckFunctionExists.c.o   -c /usr/share/cmake-2.8/Modules/CheckFunctionExists.c
Linking C executable cmTryCompileExec2090637266
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec2090637266.dir/link.txt --verbose=1
/usr/bin/cc   -DCHECK_FUNCTION_EXISTS=pthread_create    CMakeFiles/cmTryCompileExec2090637266.dir/CheckFunctionExists.c.o  -o cmTryCompileExec2090637266 -rdynamic -lpthread
make[1]: Leaving directory `/home/mpiuser/datampi-0.6.0-build/CMakeFiles/CMakeTmp'

CMakeError.log

Determining if the pthread_create exist failed with the following output:
Change Dir: /home/mpiuser/datampi-0.6.0-build/CMakeFiles/CMakeTmp

Run Build Command:/usr/bin/make "cmTryCompileExec4212361292/fast"
/usr/bin/make -f CMakeFiles/cmTryCompileExec4212361292.dir/build.make CMakeFiles/cmTryCompileExec4212361292.dir/build
make[1]: Entering directory `/home/mpiuser/datampi-0.6.0-build/CMakeFiles/CMakeTmp'
/usr/bin/cmake -E cmake_progress_report /home/mpiuser/datampi-0.6.0-build/CMakeFiles/CMakeTmp/CMakeFiles 1
Building C object CMakeFiles/cmTryCompileExec4212361292.dir/CheckSymbolExists.c.o
/usr/bin/cc    -o CMakeFiles/cmTryCompileExec4212361292.dir/CheckSymbolExists.c.o   -c /home/mpiuser/datampi-0.6.0-build/CMakeFiles/CMakeTmp/CheckSymbolExists.c
Linking C executable cmTryCompileExec4212361292
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec4212361292.dir/link.txt --verbose=1
/usr/bin/cc       CMakeFiles/cmTryCompileExec4212361292.dir/CheckSymbolExists.c.o  -o cmTryCompileExec4212361292 -rdynamic
CMakeFiles/cmTryCompileExec4212361292.dir/CheckSymbolExists.c.o: In function `main':
CheckSymbolExists.c:(.text+0x16): undefined reference to `pthread_create'
collect2: error: ld returned 1 exit status
make[1]: Leaving directory `/home/mpiuser/datampi-0.6.0-build/CMakeFiles/CMakeTmp'
make[1]: *** [cmTryCompileExec4212361292] Error 1
make: *** [cmTryCompileExec4212361292/fast] Error 2

File /home/mpiuser/datampi-0.6.0-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: /home/mpiuser/datampi-0.6.0-build/CMakeFiles/CMakeTmp

Run Build Command:/usr/bin/make "cmTryCompileExec2178398141/fast"
/usr/bin/make -f CMakeFiles/cmTryCompileExec2178398141.dir/build.make CMakeFiles/cmTryCompileExec2178398141.dir/build
make[1]: Entering directory `/home/mpiuser/datampi-0.6.0-build/CMakeFiles/CMakeTmp'
/usr/bin/cmake -E cmake_progress_report /home/mpiuser/datampi-0.6.0-build/CMakeFiles/CMakeTmp/CMakeFiles 1
Building C object CMakeFiles/cmTryCompileExec2178398141.dir/CheckFunctionExists.c.o
/usr/bin/cc   -DCHECK_FUNCTION_EXISTS=pthread_create   -o CMakeFiles/cmTryCompileExec2178398141.dir/CheckFunctionExists.c.o   -c /usr/share/cmake-2.8/Modules/CheckFunctionExists.c
Linking C executable cmTryCompileExec2178398141
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec2178398141.dir/link.txt --verbose=1
/usr/bin/cc   -DCHECK_FUNCTION_EXISTS=pthread_create    CMakeFiles/cmTryCompileExec2178398141.dir/CheckFunctionExists.c.o  -o cmTryCompileExec2178398141 -rdynamic -lpthreads
/usr/bin/ld: cannot find -lpthreads
collect2: error: ld returned 1 exit status
make[1]: Leaving directory `/home/mpiuser/datampi-0.6.0-build/CMakeFiles/CMakeTmp'
make[1]: *** [cmTryCompileExec2178398141] Error 1
make: *** [cmTryCompileExec2178398141/fast] Error 2

[Yang Redshoee]

/usr/bin/ld: cannot find -lpthreads
collect2: error: ld returned 1 exit status
make[1]: Leaving directory `/home/mpiuser/datampi-0.6.0-build/CMakeFiles/CMakeTmp'
make[1]: *** [cmTryCompileExec2178398141] Error 1
make: *** [cmTryCompileExec2178398141/fast] Error 2

..

Try to reslove   the   /usr/bin/ld: cannot find -lpthreads  problem.

Shicai Wang於 2015年1月8日星期四UTC+8上午1時22分49秒寫道：

[MPI-D]

Hi, all,

I'm sending this reply to close this issue.

Finally, CMake-2.8.9 fixed the issue.

Thanks,

DataMPI Team