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Intel-HLS / GenomicsDB

GenomicsDB
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Cmake error: cannot find MPI on macOS #187

Closed nuin closed 6 years ago

nuin commented 6 years ago

Hi

Installed all the requirements to the letter and running on problems building the application on macOS 10.13.2

cmake ../ -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr/local/bin \
    -DMPI_CC_COMPILER=/usr/local/opt/mpich/bin/mpicc -DMPI_CXX_COMPILER=/usr/local/opt/mpich/bin/mpicxx \
    -DOPENSSL_PREFIX_DIR=/usr/local/opt/openssl
-- The C compiler identification is AppleClang 9.1.0.9020039
-- The CXX compiler identification is AppleClang 9.1.0.9020039
-- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/cc
-- Check for working C compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/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: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++
-- Check for working CXX compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Performing Test test_cpp_2011
-- Performing Test test_cpp_2011 - Success
-- Could NOT find MPI_C (missing: MPI_C_WORKS)
-- Could NOT find MPI_CXX (missing: MPI_CXX_WORKS)
CMake Error at /usr/local/Cellar/cmake/3.11.1/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:137 (message):
  Could NOT find MPI (missing: MPI_C_FOUND MPI_CXX_FOUND)
Call Stack (most recent call first):
  /usr/local/Cellar/cmake/3.11.1/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:378 (_FPHSA_FAILURE_MESSAGE)
  /usr/local/Cellar/cmake/3.11.1/share/cmake/Modules/FindMPI.cmake:1663 (find_package_handle_standard_args)
  CMakeLists.txt:78 (find_package)

mpicc and mpicxx seem fine

 master ⮀ mpicc -v
mpicc for MPICH version 3.2.1
Apple LLVM version 9.1.0 (clang-902.0.39.1)
Target: x86_64-apple-darwin17.3.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
clang: warning: argument unused during compilation: '-I /usr/local/Cellar/mpich/3.2.1_1/include' [-Wunused-command-line-argument]
 master ⮀ mpicxx -v
mpicxx for MPICH version 3.2.1
Apple LLVM version 9.1.0 (clang-902.0.39.1)
Target: x86_64-apple-darwin17.3.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
clang: warning: argument unused during compilation: '-I /usr/local/Cellar/mpich/3.2.1_1/include' [-Wunused-command-line-argument]

Any help appreciated.

kgururaj commented 6 years ago

Hmm - would it be possible to attach the files CMakeFiles/CMakeOutput.log and CMakeFiles/CMakeError.log from your build directory?

nuin commented 6 years ago

Hi

Here is CmakeOutput.log

The system is: Darwin - 17.3.0 - x86_64
Compiling the C compiler identification source file "CMakeCCompilerId.c" succeeded.
Compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/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 AppleClang, found in "/Users/nuin/src/GenomicsDB/build/CMakeFiles/3.11.1/CompilerIdC/a.out"

Compiling the CXX compiler identification source file "CMakeCXXCompilerId.cpp" succeeded.
Compiler: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ 
Build flags: 
Id flags:  

The output was:
0

Compilation of the CXX compiler identification source "CMakeCXXCompilerId.cpp" produced "a.out"

The CXX compiler identification is AppleClang, found in "/Users/nuin/src/GenomicsDB/build/CMakeFiles/3.11.1/CompilerIdCXX/a.out"

Determining if the C compiler works passed with the following output:
Change Dir: /Users/nuin/src/GenomicsDB/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/make" "cmTC_4f705/fast"
/Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/cmTC_4f705.dir/build.make CMakeFiles/cmTC_4f705.dir/build
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Linking C executable cmTC_4f705
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Detecting C compiler ABI info compiled with the following output:
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Linking C executable cmTC_fe0f4
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Apple LLVM version 9.1.0 (clang-902.0.39.1)
Target: x86_64-apple-darwin17.3.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
 "/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld" -demangle -lto_library /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/libLTO.dylib -dynamic -arch x86_64 -macosx_version_min 10.13.0 -o cmTC_fe0f4 -search_paths_first -headerpad_max_install_names -v CMakeFiles/cmTC_fe0f4.dir/CMakeCCompilerABI.c.o -lSystem /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/9.1.0/lib/darwin/libclang_rt.osx.a
@(#)PROGRAM:ld  PROJECT:ld64-351.8
configured to support archs: armv6 armv7 armv7s arm64 i386 x86_64 x86_64h armv6m armv7k armv7m armv7em (tvOS)
Library search paths:
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    /usr/local/lib
Framework search paths:
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    /System/Library/Frameworks/

Parsed C implicit link information from above output:
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Detecting CXX compiler ABI info compiled with the following output:
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Detecting CXX [-std=c++11] compiler features compiled with the following output:
Change Dir: /Users/nuin/src/GenomicsDB/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/make" "cmTC_145a5/fast"
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Performing C++ SOURCE FILE Test test_cpp_2011 succeeded with the following output:
Change Dir: /Users/nuin/src/GenomicsDB/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/make" "cmTC_2dc78/fast"
/Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/cmTC_2dc78.dir/build.make CMakeFiles/cmTC_2dc78.dir/build
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Linking CXX executable cmTC_2dc78
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Source file was:
int main() { return 0; }
nuin commented 6 years ago

I don't have a CMakeError.log file

Thanks

kgururaj commented 6 years ago

That's strange - unfortunately, the CMakeOutput doesn't show any errors - could you retry the command (cmake) and see if it produces the CMakeError file? If not, would it be possible to tar up the CMakeFiles directory and attach it to this issue?

nuin commented 6 years ago

I did a clean install (from cloning) and run into the same errors. Dir is attached.

CMakeFiles.tar.gz

kgururaj commented 6 years ago

I could reproduce the error on CMake 3.11 but not on CMake 3.5 - it appears the the CMake FindMPI module has changed. I don't understand why it's failing in the new version, but here is a workaround.

bash-3.2$  /usr/local/opt/mpich/bin/mpicc -show
clang -Wl,-flat_namespace -Wl,-commons,use_dylibs -I/usr/local/Cellar/mpich/3.2_1/include -L/usr/local/Cellar/mpich/3.2_1/lib -lmpi -lpmpi

In the following command, I'm going to override the CMake FindMPI detection process

cmake  <other_args> \
   -DMPI_C_ADDITIONAL_INCLUDE_DIRS=/usr/local/opt/mpich/include/ \
   -DMPI_C_LIBRARIES="-L/usr/local/opt/mpich/lib -lmpi -lpmpi" \
   -DMPI_CXX_ADDITIONAL_INCLUDE_DIRS=/usr/local/opt/mpich/include/ \
   -DMPI_CXX_LIBRARIES="-L/usr/local/opt/mpich/lib -lmpi -lpmpi"

The above command worked for me - I will try to find out what's going on with the new CMake FindMPI detection and see if there's a simpler resolution.

kgururaj commented 6 years ago

Follow up - the above change still gave me link errors. Here is a command that works:

cmake <other_args> \
  -DCMAKE_C_COMPILER=/usr/local/opt/mpich/bin/mpicc \
  -DCMAKE_CXX_COMPILER=/usr/local/opt/mpich/bin/mpicxx

Based on the comment here, I might have to modify the CMake files - for now, the above command works (please delete your old build files first).

nuin commented 6 years ago

It worked fine this time, thanks @kgururaj

kgururaj commented 6 years ago

Just FYI - this is now fixed. If you have mpicxx in your PATH or specified via the command line flag MPI_CXX_COMPILER, the build should work