cmake error when building a C library as BPF - cmake

I would like to use a rust library that is a C bindings in Solana.
First Solana is calling the cmake of the h3 library, I am replicating the process here.
I am cloning the repo and creating a build folder
git clone --recurse-submodules https://github.com/nmandery/h3ron.git
mkdir h3ron/build
cd h3ron/build
I export the path to lld and run the cmake command very similar to solana's command (I added -v -fuse-ld=lld ) why is solana missing this one argument? it seems it needs solana's lld and not the system ld.
export PATH="/home/pc/.local/share/solana/install/releases/1.9.4/solana-release/bin/sdk/bpf/dependencies/bpf-tools/llvm/bin/:$PATH"
"cmake" "../h3ron-h3-sys/libh3" \
"-DCMAKE_INSTALL_PREFIX=./h3ron-h3-sys-df478ba73015eab9/out" \
"-DCMAKE_C_FLAGS= -ffunction-sections -fdata-sections -fPIC --target=bpfel-unknown-none -v -fuse-ld=lld" \
"-DCMAKE_C_COMPILER=/home/pc/.local/share/solana/install/releases/1.9.4/solana-release/bin/sdk/bpf/dependencies/bpf-tools/llvm/bin/clang" \
"-DCMAKE_CXX_FLAGS= -ffunction-sections -fdata-sections -fPIC -v" \
"-DCMAKE_CXX_COMPILER=/usr/bin/c++" \
"-DCMAKE_ASM_FLAGS= -ffunction-sections -fdata-sections -fPIC --target=bpfel-unknown-unknown -v" \
"-DCMAKE_ASM_COMPILER=/home/pc/.local/share/solana/install/releases/1.9.4/solana-release/bin/sdk/bpf/dependencies/bpf-tools/llvm/bin/clang" \
"-DCMAKE_BUILD_TYPE=Release"
The error:
Target: bpfel-unknown-none
Thread model: posix
InstalledDir: /home/pc/.local/share/solana/install/releases/1.9.4/solana-release/bin/sdk/bpf/dependencies/bpf-tools/llvm/bin
"/usr/bin/gcc" -fuse-ld=lld -rdynamic -o cmTC_26933 CMakeFiles/cmTC_26933.dir/testCCompiler.c.o
ld.lld: error: CMakeFiles/cmTC_26933.dir/testCCompiler.c.o is incompatible with elf64-x86-64
collect2: error: ld returned 1 exit status
Note: The system ld would generate this error /usr/bin/ld: unknown architecture of input file CMakeFiles/cmTC_5c450.dir/testCCompiler.c.o' is incompatible with i386:x86-64 output
any idea?

Related

CMake ninja custom target used as pre-build command modifies the files but ninja see the change of the depndecies during next build

I run some command before the actual build
add_custom_target("${PROJECT_BUILD_NUM_FILE}"
COMMAND ${PROJECT_BUILD_NUM_UPDATE} "-p" "-x" -f ${PROJECT_SOURCE_DIR}/${MAIN_PATH}/${BOARD_NAME}/${PROJECT_BUILD_NUM_FILE}
)
add_dependencies(${EXECUTABLE_NAME} "${PROJECT_BUILD_NUM_FILE}" )
When I build first time (the project was build before)
>------ Build started: Project: CMakeLists, Configuration: Debug ------
[1/1] cmd.exe /C "cd /D C:\Users\Piotr\git\gPIMS-EG\out\build\IoT-Debug && C:\Users\Piotr\git\gPIMS-EG\stm-libs\pc-exe\buildnum.exe -p -x -f C:/Users/Piotr/git/gPIMS-EG/src/EG/BuildID.h"
Build number file used:C:/Users/Piotr/git/gPIMS-EG/src/EG/BuildID.h
Build file updated: Build Number: 22 DateCode: 0x1d6d
Build succeeded.
BuildID.h file was modified and saved. Modification date is set correctly.
On the second build it behaves correctly
>------ Build started: Project: CMakeLists, Configuration: Debug ------
[1/4] cmd.exe /C "cd /D C:\Users\Piotr\git\gPIMS-EG\out\build\IoT-Debug && C:\Users\Piotr\git\gPIMS-EG\stm-libs\pc-exe\buildnum.exe -p -x -f C:/Users/Piotr/git/gPIMS-EG/src/EG/BuildID.h"
Build number file used:C:/Users/Piotr/git/gPIMS-EG/src/EG/BuildID.h
Build file updated: Build Number: 23 DateCode: 0x1d6d
[2/4] C:\PROGRA~2\Atollic\TRUEST~1.0\ARMTools\bin\AR097D~1.EXE -DALLOW_SOFTWARE_BKPTS=1 -DARM_MATH_CM4 -DBOOTLOADER_VERSION=1 -DCOMPILE_FOR_EG=1 -DDEBUGFILEWRITE=1 -DDEBUG_RUN_WITHOUT_CHECKS=1 -DFORCE_CUBE_USB -DHSE_VALUE=8000000UL -DSLOWSPIDEBUG=0 -DSTM32L -DSTM32L476xx -DSTM32L4xx -DUSE_EMBEDDED_PHY=1 -DUSE_FULL_ASSERT -DUSE_FULL_LL_DRIVER="" -DUSE_HAL_DRIVER -DUSE_SWOTRACE=1 -DUSE_USB_OTG_FS=1 -DUSE_USB_OTG_HS=1 -D_DEBUG=1 -D_GNU_SOURCE=1 -D__USE_SIMPLE_SWO=0 -I../../../src -I../../../src/EG -I../../../src/ZM -I../../../src/inc -I../../../stm-libs/inc -I../../../stm-libs/Drivers -I../../../stm-libs/Services -I../../../stm-libs/Services/Utils -I../../../stm-libs/RTOS/Source/include -I../../../stm-libs/RTOS/Source/portable/GCC/ARM_CM4F -I../../../stm-libs/Libraries/CMSIS/Include -I../../../stm-libs/Libraries/CMSIS/Device/ST/STM32L4xx/Include -I../../../stm-libs/Libraries/CryptoLib/Inc -I../../../stm-libs/Libraries/CryptoLib/Inc/RNG -I../../../stm-libs/drivers/USBD -I../../../stm-libs/Libraries/Middlewares/ST/STM32_USB_Device_Library/Core/Inc -I../../../stm-libs/Libraries/USB/Device/Class/CDC/Inc -I../../../stm-libs/Libraries/USB/Device/Class/MSC_HID/Inc -I../../../stm-libs/Libraries/USB/Device/Core/Inc -I../../../stm-libs/Libraries/lwip/ports/STM32F4x7 -I../../../stm-libs/Libraries/lwip/ports/STM32F4x7/arch -I../../../stm-libs/Libraries/lwip/src -I../../../stm-libs/Libraries/lwip/src/include -I../../../stm-libs/drivers/USBH -I../../../stm-libs/Libraries/USB/Host/Class/AUDIO/Inc -I../../../stm-libs/Libraries/USB/Host/Class/CDC/Inc -I../../../stm-libs/Libraries/USB/Host/Class/HID/Inc -I../../../stm-libs/Libraries/USB/Host/Class/MSC/Inc -I../../../stm-libs/Libraries/USB/Host/Class/MTP/Inc -I../../../stm-libs/Libraries/USB/Host/Core/Inc -I../../../stm-libs/Libraries/USB/Host/Class/Template/Inc -I../../../stm-libs/Libraries/lwip/ports/STM32F4x7/FreeRTOS -I../../../stm-libs/Libraries/misc -I../../../stm-libs/Libraries/FatFs/src -I../../../stm-libs/Libraries/littleFS -I../../../stm-libs/Apps -I../../../stm-libsApps/SeqZM -I../../../stm-libs/Libraries/libc_e -I../../../stm-libs/Libraries -I../../../stm-hal-l4/Inc/Legacy -I../../../stm-hal-l4/Inc -I../../../stm-libs/Apps/Other -mthumb -mcpu=cortex-m4 -mfloat-abi=hard -mfpu=fpv4-sp-d16 -Og -g3 -T"C:/Users/Piotr/git/gPIMS-EG/src/EG/startup/EG.ld" -L"C:/Users/Piotr/git/gPIMS-EG/stm-libs/Libraries/CryptoLib" -lSTM32CryptographicV3.0.0_CM4_GCC_FPU -specs=nosys.specs -specs=nano.specs -Wl,-Map="EG.map" -static -Wl,-u,Reset_Handler -Wl,--gc-sections -Wl,--defsym=malloc_getpagesize_P=0x80 -Wl,--start-group -lc -lm -Wl,--end-group -ffunction-sections -fdata-sections -g -MD -MT CMakeFiles/GCEG-FW.dir/stm-libs/Apps/common/SC_Ver.c.obj -MF CMakeFiles\GCEG-FW.dir\stm-libs\Apps\common\SC_Ver.c.obj.d -o CMakeFiles/GCEG-FW.dir/stm-libs/Apps/common/SC_Ver.c.obj -c ../../../stm-libs/Apps/common/SC_Ver.c
In file included from ../../../stm-libs/Apps/common/SC_Ver.c:9:0:
C:\Users\Piotr\git\gPIMS-EG\stm-libs\Drivers\CAN-COB.h(267,2): warning GF07C7A44: #warning added to compile BP to change [-Wcpp]
#warning added to compile BP to change
^~~~~~~
[3/4] C:\PROGRA~2\Atollic\TRUEST~1.0\ARMTools\bin\AR097D~1.EXE -DALLOW_SOFTWARE_BKPTS=1 -DARM_MATH_CM4 -DBOOTLOADER_VERSION=1 -DCOMPILE_FOR_EG=1 -DDEBUGFILEWRITE=1 -DDEBUG_RUN_WITHOUT_CHECKS=1 -DFORCE_CUBE_USB -DHSE_VALUE=8000000UL -DSLOWSPIDEBUG=0 -DSTM32L -DSTM32L476xx -DSTM32L4xx -DUSE_EMBEDDED_PHY=1 -DUSE_FULL_ASSERT -DUSE_FULL_LL_DRIVER="" -DUSE_HAL_DRIVER -DUSE_SWOTRACE=1 -DUSE_USB_OTG_FS=1 -DUSE_USB_OTG_HS=1 -D_DEBUG=1 -D_GNU_SOURCE=1 -D__USE_SIMPLE_SWO=0 -I../../../src -I../../../src/EG -I../../../src/ZM -I../../../src/inc -I../../../stm-libs/inc -I../../../stm-libs/Drivers -I../../../stm-libs/Services -I../../../stm-libs/Services/Utils -I../../../stm-libs/RTOS/Source/include -I../../../stm-libs/RTOS/Source/portable/GCC/ARM_CM4F -I../../../stm-libs/Libraries/CMSIS/Include -I../../../stm-libs/Libraries/CMSIS/Device/ST/STM32L4xx/Include -I../../../stm-libs/Libraries/CryptoLib/Inc -I../../../stm-libs/Libraries/CryptoLib/Inc/RNG -I../../../stm-libs/drivers/USBD -I../../../stm-libs/Libraries/Middlewares/ST/STM32_USB_Device_Library/Core/Inc -I../../../stm-libs/Libraries/USB/Device/Class/CDC/Inc -I../../../stm-libs/Libraries/USB/Device/Class/MSC_HID/Inc -I../../../stm-libs/Libraries/USB/Device/Core/Inc -I../../../stm-libs/Libraries/lwip/ports/STM32F4x7 -I../../../stm-libs/Libraries/lwip/ports/STM32F4x7/arch -I../../../stm-libs/Libraries/lwip/src -I../../../stm-libs/Libraries/lwip/src/include -I../../../stm-libs/drivers/USBH -I../../../stm-libs/Libraries/USB/Host/Class/AUDIO/Inc -I../../../stm-libs/Libraries/USB/Host/Class/CDC/Inc -I../../../stm-libs/Libraries/USB/Host/Class/HID/Inc -I../../../stm-libs/Libraries/USB/Host/Class/MSC/Inc -I../../../stm-libs/Libraries/USB/Host/Class/MTP/Inc -I../../../stm-libs/Libraries/USB/Host/Core/Inc -I../../../stm-libs/Libraries/USB/Host/Class/Template/Inc -I../../../stm-libs/Libraries/lwip/ports/STM32F4x7/FreeRTOS -I../../../stm-libs/Libraries/misc -I../../../stm-libs/Libraries/FatFs/src -I../../../stm-libs/Libraries/littleFS -I../../../stm-libs/Apps -I../../../stm-libsApps/SeqZM -I../../../stm-libs/Libraries/libc_e -I../../../stm-libs/Libraries -I../../../stm-hal-l4/Inc/Legacy -I../../../stm-hal-l4/Inc -I../../../stm-libs/Apps/Other -mthumb -mcpu=cortex-m4 -mfloat-abi=hard -mfpu=fpv4-sp-d16 -Og -g3 -T"C:/Users/Piotr/git/gPIMS-EG/src/EG/startup/EG.ld" -L"C:/Users/Piotr/git/gPIMS-EG/stm-libs/Libraries/CryptoLib" -lSTM32CryptographicV3.0.0_CM4_GCC_FPU -specs=nosys.specs -specs=nano.specs -Wl,-Map="EG.map" -static -Wl,-u,Reset_Handler -Wl,--gc-sections -Wl,--defsym=malloc_getpagesize_P=0x80 -Wl,--start-group -lc -lm -Wl,--end-group -ffunction-sections -fdata-sections -g -MD -MT CMakeFiles/GCEG-FW.dir/stm-libs/Apps/WaveMC3/waveMC3SeqGUI.c.obj -MF CMakeFiles\GCEG-FW.dir\stm-libs\Apps\WaveMC3\waveMC3SeqGUI.c.obj.d -o CMakeFiles/GCEG-FW.dir/stm-libs/Apps/WaveMC3/waveMC3SeqGUI.c.obj -c ../../../stm-libs/Apps/WaveMC3/waveMC3SeqGUI.c
In file included from ../../../stm-libs/Drivers/CAN-G3M.h:31:0,
from ../../../stm-libs/Drivers/ioCmd.h:12,
from ../../../stm-libs/Services/srvCmd.h:9,
from ../../../src/EG/../ZM/zmServices.h:10,
from ../../../src/EG/ourServices.h:12,
from ../../../stm-libs/Apps/WaveMC3/waveMC3SeqGUI.c:5:
C:\Users\Piotr\git\gPIMS-EG\stm-libs\Drivers\CAN-COB.h(267,2): warning GF07C7A44: #warning added to compile BP to change [-Wcpp]
#warning added to compile BP to change
^~~~~~~
[4/4] cmd.exe /C "cd . && C:\PROGRA~2\Atollic\TRUEST~1.0\ARMTools\bin\AR097D~1.EXE -mthumb -mcpu=cortex-m4 -mfloat-abi=hard -mfpu=fpv4-sp-d16 -Og -g3 -T"C:/Users/Piotr/git/gPIMS-EG/src/EG/startup/EG.ld" -L"C:/Users/Piotr/git/gPIMS-EG/stm-libs/Libraries/CryptoLib" -lSTM32CryptographicV3.0.0_CM4_GCC_FPU -specs=nosys.specs -specs=nano.specs -Wl,-Map="EG.map" -static -Wl,-u,Reset_Handler -Wl,--gc-sections -Wl,--defsym=malloc_getpagesize_P=0x80 -Wl,--start-group -lc -lm -Wl,--end-group -ffunction-sections -fdata-sections -g #CMakeFiles\GCEG-FW.rsp -o GCEG-FW.elf && cmd.exe /C "cd /D C:\Users\Piotr\git\gPIMS-EG\out\build\IoT-Debug && "C:\Program Files (x86)\Atollic\TrueSTUDIO for STM32 9.3.0\ARMTools\bin\arm-atollic-eabi-objcopy.exe" GCEG-FW.elf --output-target=binary GCEG-FW.bin -j .isr_vector -j .VERSION_INFO -j .text -j .rodata -j .ARM.extab -j .ARM -j .preinit_array -j .init_array -j .fini_array -j .data -j .RAM_VectorTable -j .RAM_DATAfunctions -j .RAM_functions -v && "C:\Program Files (x86)\Atollic\TrueSTUDIO for STM32 9.3.0\ARMTools\bin\arm-atollic-eabi-size.exe" GCEG-FW.elf --format=Berkeley""
copy from `GCEG-FW.elf' [elf32-littlearm] to `GCEG-FW.bin' [binary]
text data bss dec hex filename
210428 36680 54020 301128 49848 GCEG-FW.elf
Build succeeded.
It looks like ninja is checking dependencies before the actual build starts and ignores meanwhile file changed. Is there any way to force cmake/ninja to recheck dependecies after custom target is build (ie prgram that thenges the build is run).
It looks like ninja is checking dependencies before the actual build starts and ignores meanwhile file change
Hey! Yes. Because DEPFILEs from C source files are generated at the same time as they are compiled, cmake has no way to know beforehand which file depends on which. It would have to do two passes - first to get dependencies and then to compile (which would be a nice feature, but actually hard to implement). It happens in one pass during compilation (-MD -MT flags), so cmake has no way of knowing that one file depends on that header. I also advise:
Do not modify files in your source tree. Keep all changes in BINARY_DIR.
Do not modify files. Generate new files. It's easier and generally, less state = less problems.
Try it such:
# Inside binary_dir
set(PROJECT_BUILD_NUM_FILE ${CMAKE_CURRENT_BINARY_DIR}/gen/buildid_gen.h)
# Add #include <buildid_gen.h> to your buildid.h
add_custom_command(
OUTPUT ${PROJECT_BUILD_NUM_FILE}
COMMAND ${PROJECT_BUILD_NUM_UPDATE} "-p" "-x" -f ${PROJECT_BUILD_NUM_FILE}
DEPENDS ${PROJECT_BUILD_NUM_UPDATE}
)
add_custom_target(buildid_gen
COMMENT "Yooohooo!"
DEPENDS ${PROJECT_BUILD_NUM_FILE}
)
add_executable(${EXECUTABLE_NAME} ${PROJECT_BUILD_NUM_FILE} ${some_other_sources})
target_add_include_directories(${EXECTABLE_NAME} PUBLIC
# add include directory, so that buildid_gen is found
${CMAKE_CURRENT_BINARY_DIR}/gen
)
# this *helps*
add_dependencies(${EXECUTABLE_NAME} buildid_gen)
Is there any way to force cmake/ninja to recheck dependecies after custom target is build (ie prgram that thenges the build is run).
The real proper way ™ would be to manually track all files that depend on the file (you could think of grep -l '#include <buildid_gen.h> to get the list files) and communicate to cmake the dependency relation:
add_source_file_properties(${sources_that_include_buildid_gen} PROPERTIES OBJECT_DEPENDS ${PROJECT_BUILD_NUM_FILE})
Tracking dependencies is easier if you use a runtime interface (ie. long get_build_id();) cause then only one .c file that implements the interface will depend on the generated file.
There are also some projects that are compiled in two passes because of such dependencies, you have to first cmake .. --target buildid_gen and then cmake .. --target actually_compile each time you compile.
Also maybe execute_process is more appropriate if the file is setup once per build.

Percona5.7 cmake failed on centos 7

I get the source code of percona-server from github. And I install boost 1.59 and gcc gcc-c ncurses-devel. I enter the directory of percona-server and run "cmake --DWITH_BOOST=/data/boost" but get the following error. I cannot find some solution so I came to here. Thanks!!
-- Performing Test HAVE_UNUSED_PARAMETER - Success
-- Googletest was not found. gtest-based unit tests will be disabled. You can run cmake . -DENABLE_DOWNLOADS=1 to automatically download and build required components from source.
-- If you are inside a firewall, you may need to use an https proxy: export https_proxy=http://example.com:80
-- Performing Test HAVE_MISLEADING_INDENTATION
-- Performing Test HAVE_MISLEADING_INDENTATION - Failed
-- executable target mysqld debug_target /home/teg/Downloads/debug/sql/mysqld
-- Library mysqlserver depends on OSLIBS -lpthread;/usr/lib64/libz.so;m;rt;crypt;dl;aio;numa
-- MERGE_CONVENIENCE_LIBRARIES TARGET mysqlserver
-- MERGE_CONVENIENCE_LIBRARIES LIBS dbug;strings;regex;mysys;mysys_ssl;vio;/usr/lib64/libz.so;yassl;taocrypt;crypt;dl;archive_embedded;b lackhole_embedded;csv_embedded;federated_embedded; heap_embedded;innobase_embedded;lz4_lib;numa;myisa m_embedded;myisammrg_embedded;partition_embedded;n gram_parser_embedded;sql_embedded
-- MERGE_CONVENIENCE_LIBRARIES MYLIBS dbug;strings;regex;mysys;mysys_ssl;vio;yassl;taocr ypt;archive_embedded;blackhole_embedded;csv_embedd ed;federated_embedded;heap_embedded;innobase_embed ded;lz4_lib;myisam_embedded;myisammrg_embedded;par tition_embedded;ngram_parser_embedded;sql_embedded
-- library target mysqlserver debug_target /home/teg/Downloads/debug/archive_output_directory/libmysqld.a
-- INSTALL perconaserverclient.pc lib/pkgconfig
-- Skipping deb packaging on unsupported platform Core.
-- CMAKE_BUILD_TYPE: RelWithDebInfo
-- COMPILE_DEFINITIONS: _GNU_SOURCE;_FILE_OFFSET_BITS=64;HAVE_CONFIG_H;HAV E_LIBEVENT1
-- CMAKE_C_FLAGS: -Wall -Wextra -Wformat-security -Wvla -Wwrite-strings -Wdeclaration-after-statement
-- CMAKE_CXX_FLAGS: -std=gnu++03 -Wall -Wextra -Wformat-security -Wvla -Woverloaded-virtual -Wno-unused-parameter
-- CMAKE_C_LINK_FLAGS:
-- CMAKE_CXX_LINK_FLAGS:
-- CMAKE_C_FLAGS_RELWITHDEBINFO: -O3 -D_FORTIFY_SOURCE=2 -g -fabi-version=2 -fno-omit-frame-pointer -fno-strict-aliasing -DDBUG_OFF -DNDEBUG
-- CMAKE_CXX_FLAGS_RELWITHDEBINFO: -O3 -D_FORTIFY_SOURCE=2 -g -fabi-version=2 -fno-omit-frame-pointer -fno-strict-aliasing -DDBUG_OFF -DNDEBUG
-- Configuring incomplete, errors occurred!
See also "/home/teg/Downloads/percona-server-5.7/CMakeFiles/CMakeOutput.log".
See also "/home/teg/Downloads/percona-server-5.7/CMakeFiles/CMakeError.log".
.................................................. .........................
And I open the /home/teg/Downloads/percona-server-5.7/CMakeFiles/CMakeError.log and find the following errors. There are too many errors and I only list part of it.
Run Build Command:/usr/bin/gmake "cmTryCompileExec1295500228/fast"
/usr/bin/gmake -f CMakeFiles/cmTryCompileExec1295500228.dir/build.make CMakeFiles/cmTryCompileExec1295500228.dir/build
gmake[1]: Entering directory `/home/teg/Downloads/percona-server-5.7/CMakeFiles/CMakeTmp'
/usr/bin/cmake -E cmake_progress_report /home/teg/Downloads/percona-server-5.7/CMakeFiles/CMakeTmp/CMakeFiles 1
Building C object CMakeFiles/cmTryCompileExec1295500228.dir/CheckSymbolExists.c.o
/usr/bin/cc -o CMakeFiles/cmTryCompileExec1295500228.dir/CheckSymbolExists.c.o -c /home/teg/Downloads/percona-server-5.7/CMakeFiles/CMakeTmp/CheckSymbolExists.c
Linking C executable cmTryCompileExec1295500228
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec1295500228.dir/link.txt --verbose=1
/usr/bin/cc CMakeFiles/cmTryCompileExec1295500228.dir/CheckSymbolExists.c.o -o cmTryCompileExec1295500228 -rdynamic
CMakeFiles/cmTryCompileExec1295500228.dir/CheckSymbolExists.c.o: In function `main':
CheckSymbolExists.c.text+0x16): undefined reference to `pthread_create'
collect2: error: ld returned 1 exit status
gmake[1]: Leaving directory `/home/teg/Downloads/percona-server-5.7/CMakeFiles/CMakeTmp'
gmake[1]: *** [cmTryCompileExec1295500228] Error 1
gmake: *** [cmTryCompileExec1295500228/fast] Error 2
File /home/teg/Downloads/percona-server-5.7/CMakeFiles/CMakeTmp/CheckSymbolExists.c:
Run Build Command:/usr/bin/gmake "cmTryCompileExec1916958743/fast"
/usr/bin/gmake -f CMakeFiles/cmTryCompileExec1916958743.dir/build.make CMakeFiles/cmTryCompileExec1916958743.dir/build
gmake[1]: Entering directory `/home/teg/Downloads/percona-server-5.7/CMakeFiles/CMakeTmp'
/usr/bin/cmake -E cmake_progress_report /home/teg/Downloads/percona-server-5.7/CMakeFiles/CMakeTmp/CMakeFiles 1
Building C object CMakeFiles/cmTryCompileExec1916958743.dir/CheckFunctionExists.c.o
/usr/bin/cc -DCHECK_FUNCTION_EXISTS=pthread_create -o CMakeFiles/cmTryCompileExec1916958743.dir/CheckFunctionExists.c.o -c /usr/share/cmake/Modules/CheckFunctionExists.c
Linking C executable cmTryCompileExec1916958743
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec1916958743.dir/link.txt --verbose=1
/usr/bin/cc -DCHECK_FUNCTION_EXISTS=pthread_create CMakeFiles/cmTryCompileExec1916958743.dir/CheckFunctionExists.c.o -o cmTryCompileExec1916958743 -rdynamic -lpthreads
/usr/bin/ld: cannot find -lpthreads
collect2: error: ld returned 1 exit status
gmake[1]: Leaving directory `/home/teg/Downloads/percona-server-5.7/CMakeFiles/CMakeTmp'
gmake[1]: *** [cmTryCompileExec1916958743] Error 1
gmake: *** [cmTryCompileExec1916958743/fast] Error 2
Determining if the function floor exists failed with the following output:
Change Dir: /home/teg/Downloads/percona-server-5.7/CMakeFiles/CMakeTmp
Run Build Command:/usr/bin/gmake "cmTryCompileExec1596718479/fast"
/usr/bin/gmake -f CMakeFiles/cmTryCompileExec1596718479.dir/build.make CMakeFiles/cmTryCompileExec1596718479.dir/build
gmake[1]: Entering directory `/home/teg/Downloads/percona-server-5.7/CMakeFiles/CMakeTmp'
/usr/bin/cmake -E cmake_progress_report /home/teg/Downloads/percona-server-5.7/CMakeFiles/CMakeTmp/CMakeFiles 1
Building C object CMakeFiles/cmTryCompileExec1596718479.dir/CheckFunctionExists.c.o
/usr/bin/cc -DCHECK_FUNCTION_EXISTS=floor -o CMakeFiles/cmTryCompileExec1596718479.dir/CheckFunctionExists.c.o -c /usr/share/cmake/Modules/CheckFunctionExists.c
<command-line>:0:23: warning: conflicting types for built-in function ‘floor’ [enabled by default]
/usr/share/cmake/Modules/CheckFunctionExists.c:3:6: note: in expansion of macro ‘CHECK_FUNCTION_EXISTS’
char CHECK_FUNCTION_EXISTS();
^
Linking C executable cmTryCompileExec1596718479
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec1596718479.dir/link.txt --verbose=1
/usr/bin/cc -DCHECK_FUNCTION_EXISTS=floor CMakeFiles/cmTryCompileExec1596718479.dir/CheckFunctionExists.c.o -o cmTryCompileExec1596718479 -rdynamic
CMakeFiles/cmTryCompileExec1596718479.dir/CheckFunctionExists.c.o: In function `main':
CheckFunctionExists.c.text+0x15): undefined reference to `floor'
collect2: error: ld returned 1 exit status
gmake[1]: Leaving directory `/home/teg/Downloads/percona-server-5.7/CMakeFiles/CMakeTmp'
gmake[1]: *** [cmTryCompileExec1596718479] Error 1
gmake: *** [cmTryCompileExec1596718479/fast] Error 2
it seems you haven't all needed dependencies installed.
These are the steps which are needed:
sudo yum install epel-release
sudo yum install git gcc gcc-c++ openssl check cmake bison boost-devel asio-devel
libaio-devel ncurses-devel readline-devel pam-devel wget perl-Env time numactl-devel
rpmdevtools rpm-build curl-devel
git clone https://github.com/percona/percona-server.git
cd percona-server
git submodule init
git submodule update
cmake . -DDOWNLOAD_BOOST=1 -DWITH_BOOST=<PATCH_TO_BOOST_DIR>
Then boost will be downloaded automatically

Building tensorflow from source meets error: C++ compilation of rule '#jemalloc//:jemalloc' failed

I'm attempting to build tensorflow from source on CentOS 6.2 using gcc. I updated gcc globally from 4.6.6 to 5.2.0, so that may be causing some problems. Glibc 2.17 is in a local directory, but the version of the system default Glibc is 2.12.
I get the following error:
ERROR: /usr/local/app/.cache/bazel/_bazel_mqq/51871d27dfe77ebce0294c6560736a2c/external/jemalloc/BUILD:10:1: C++ compilation of rule '#jemalloc//:jemalloc' failed: gcc failed: error executing command
(cd /usr/local/app/.cache/bazel/_bazel_mqq/51871d27dfe77ebce0294c6560736a2c/execroot/tensorflow && \
exec env - \
PATH=/data6/jimpan/env/java/jdk1.8.0_131/bin:/data6/jimpan/env/python3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/usr/local/jdk/bin:/usr/local/jdk/jre/bin:/opt/CollabNet_Subversion/bin/:/usr/local/app/java/bin:/usr/local/app/bin \
PWD=/proc/self/cwd \
PYTHON_BIN_PATH=/data6/jimpan/env/python3/bin/python3 \
PYTHON_LIB_PATH=/data6/jimpan/env/python3/lib/python3.5/site-packages \
TF_NEED_CUDA=0 \
TF_NEED_OPENCL=0 \
/usr/local/bin/gcc -U_FORTIFY_SOURCE -fstack-protector -Wall -B/usr/local/bin -B/usr/bin -Wunused-but-set-parameter -Wno-free-nonheap-object -fno-omit-frame-pointer -g0 -O2 '-D_FORTIFY_SOURCE=1' -DNDEBUG -ffunction-sections -fdata-sections '-mcpu=native' -MD -MF bazel-out/local-py3-opt/bin/external/jemalloc/_objs/jemalloc/external/jemalloc/src/pages.pic.d -fPIC -iquote external/jemalloc -iquote bazel-out/local-py3-opt/genfiles/external/jemalloc -iquote external/bazel_tools -iquote bazel-out/local-py3-opt/genfiles/external/bazel_tools -isystem external/jemalloc/include -isystem bazel-out/local-py3-opt/genfiles/external/jemalloc/include -isystem external/bazel_tools/tools/cpp/gcc3 -O3 -funroll-loops -D_GNU_SOURCE -D_REENTRANT -fno-canonical-system-headers -Wno-builtin-macro-redefined '-D__DATE__="redacted"' '-D__TIMESTAMP__="redacted"' '-D__TIME__="redacted"' -c external/jemalloc/src/pages.c -o bazel-out/local-py3-opt/bin/external/jemalloc/_objs/jemalloc/external/jemalloc/src/pages.pic.o): com.google.devtools.build.lib.shell.BadExitStatusException: Process exited with status 1.
gcc: warning: '-mcpu=' is deprecated; use '-mtune=' or '-march=' instead
external/jemalloc/src/pages.c: In function 'je_pages_huge':
external/jemalloc/src/pages.c:203:30: error: 'MADV_HUGEPAGE' undeclared (first use in this function)
return (madvise(addr, size, MADV_HUGEPAGE) != 0);
^
external/jemalloc/src/pages.c:203:30: note: each undeclared identifier is reported only once for each function it appears in
external/jemalloc/src/pages.c: In function 'je_pages_nohuge':
external/jemalloc/src/pages.c:217:30: error: 'MADV_NOHUGEPAGE' undeclared (first use in this function)
return (madvise(addr, size, MADV_NOHUGEPAGE) != 0);
^
external/jemalloc/src/pages.c: In function 'je_pages_huge':
external/jemalloc/src/pages.c:207:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
external/jemalloc/src/pages.c: In function 'je_pages_nohuge':
external/jemalloc/src/pages.c:221:1: warning: control reaches end of non-void function [-Wreturn-type]
}
^
/usr/local/app is the $HOME path of my system.
I guess the problem lies in gcc, but I'm stuck now and don't know how to proceed.
It seems that jemalloc's build is misconfigured (it's missing MADV_NOHUGEPAGE define). I found this tensorflow issue that is related.

Error linking with clang+llvm

I am trying to apply LLVM optimizations to a few Image Feature Extraction algorithms which have been implemented using openCV. The LLVM-based profiler works fine with simple programs (For instance, HelloWorld), and the feature extraction algorithms too work separately as expected.
However I was unable to use the profiler for the algorithms and got the following error while linking the OpenCV libraries to the optimized code.
gcc version 4.6.3 (Ubuntu/Linaro 4.6.3-1ubuntu5)
COLLECT_GCC_OPTIONS='-v' '-g' '-L/home/silky/opencv/share/OpenCV/3rdparty/lib' '- L/home/silky/opencv/OpenCVInstall/x86/lib' '-shared-libgcc' '-mtune=generic' '-march=x86-64' as --gdwarf2 --64 -o /tmp/ccAhPffW.o out.s
COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/4.6/:/usr/lib/gcc/x86_64-linux-gnu/4.6/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/4.6/:/usr/lib/gcc/x86_64-linux-gnu/
LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/4.6/:/usr/lib/gcc/x86_64-linux-gnu/4.6/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/4.6/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/4.6/../../../:/lib/:/usr/lib/
COLLECT_GCC_OPTIONS='-v' '-g' '-L/home/silky/opencv/share/OpenCV/3rdparty/lib' '-L/home/silky/opencv/OpenCVInstall/x86/lib' '-shared-libgcc' '-mtune=generic' '-march=x86-64'
/usr/lib/gcc/x86_64-linux-gnu/4.6/collect2 --sysroot=/ --build-id --no-add-needed --as-needed --eh-frame-hdr -m elf_x86_64 --hash-style=gnu -dynamic-linker /lib64/ld-linux-x86-64.so.2 -z relro /usr/lib/gcc/x86_64-linux-gnu/4.6/../../../x86_64-linux-gnu/crt1.o /usr/lib/gcc/x86_64-linux-gnu/4.6/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/4.6/crtbegin.o -L/home/silky/opencv/share/OpenCV/3rdparty/lib -L/home/silky/opencv/OpenCVInstall/x86/lib -L/usr/lib/gcc/x86_64-linux-gnu/4.6 -L/usr/lib/gcc/x86_64-linux-gnu/4.6/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/4.6/../../../../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/4.6/../../.. /tmp/ccAhPffW.o -lpthread -lrt -lopencv_calib3d -lopencv_core -lopencv_features2d -lopencv_flann -lopencv_highgui -lopencv_imgproc -lopencv_ml -lopencv_objdetect -lopencv_video -lopencv_nonfree -lstdc++ -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc /usr/lib/gcc/x86_64-linux-gnu/4.6/crtend.o /usr/lib/gcc/x86_64-linux-gnu/4.6/../../../x86_64-linux-gnu/crtn.o
/tmp/ccAhPffW.o:(.debug_info+0x49a14): undefined reference to `.Lline_table_start1'
collect2: ld returned 1 exit status
I've used the following commands to compile and link the files.
clang -emit-llvm -c -Wall -g -O0 -DCLOCK_GETTIME_TIMING -DOPENCV_2_4 -I/home/opencv/OpenCVInstall/x86/include -o ThreadManager.bc FeatureExtraction/ThreadManager.cpp
clang -emit-llvm -c -Wall -g -O0 -DCLOCK_GETTIME_TIMING -DOPENCV_2_4 -I/home/opencv/OpenCVInstall/x86/include -o FeatureExtraction.bc FeatureExtraction/FeatureExtraction.cpp
llvm-link FeatureExtraction.bc ThreadManager.bc -o FE.bc
clang $CFLAGS -o profiler.o cacheSim.cpp //LLVM profiler
opt -load /home/llvm/llvm/Debug+Asserts/lib/cacheProf.so -cacheProf FE.bc>out.bc
llc FE.bc -o out.s
g++ -v -g out.s profiler.o -L/home/opencv/share/OpenCV/3rdparty/lib -L/home/opencv/OpenCVInstall/x86/lib -lpthread -lrt -lopencv_calib3d -lopencv_core -lopencv_features2d -lopencv_flann -lopencv_highgui -lopencv_imgproc -lopencv_ml -lopencv_objdetect -lopencv_video -lopencv_nonfree
Could some one please tell me if I am linking the files or loading the files in a wrong way?
Is clang compilation different from how g++ works?

Trouble with g++ & libpqxx lib

I've very simple example, and can't correctly build it, I was using next arguments:
g++ -lpq -libpqxx -Wall -o "pg" "pg.cpp" (in dir: /home/user)
/usr/lib/gcc/i586-suse-linux/4.5/../../../../i586-suse-linux/bin/ld: cannot find -lpq
collect2: ld returned 1 exit status
or
returned 1 exit status g++ -libpqxx -Wall -o "pg" "pg.cpp"
(in dir: /home/user)
/usr/lib/gcc/i586-suse-linux/4.5/../../../../i586-suse-linux/bin/ld:
cannot find -libpqxx collect2: ld
but everywere had error.
libpqxx succ installed
#lisuse-home:~> locate libpqxx | grep /lib/
/usr/lib/libpqxx-3.1.so
/usr/lib/libpqxx.la
/usr/lib/libpqxx.so
/usr/lib/pkgconfig/libpqxx.pc
g++ filename.cpp -o target -lpqxx
-lpqxx should take care of -lpq. If for some reason it does not find pq, find pq and put it in the same directory as pqxx.
compiling g++ -libpqxx-3.1 -Wall -c "%f"
building g++ -Wall -o "%e" /usr/lib/libpqxx-3.1.so "%f"