Problem with running binary or compiling cas-offinder with Linux Catalyst on Ubuntu 14.04

[harijay]

Hello, Sorry to email this in as an issue but I am having some issues getting cas-offinder running on my system.

When I try the binary I get the message:

hari@hjubuntu:~/cas-offinder$ ./cas-offinder 
clGetPlatformIDs Failed: -1001

When I tried compiling I get the message:

cmake -DOPENCL_INCLUDE_DIRS=/opt/AMDAPPSDK-3.0/include  -DOPENCL_LIBRARIES=/opt/AMDAPPSDK-3.0/lib/x86_64/libOpenCL.so .

hari@hjubuntu:~/cas-offinder$ make
Scanning dependencies of target cas-offinder
[ 25%] Building CXX object CMakeFiles/cas-offinder.dir/main.cpp.o
[ 50%] Building CXX object CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o
In file included from /home/hari/cas-offinder/cas-offinder.cpp:4:0:
/home/hari/cas-offinder/oclfunctions.h: In function ‘_cl_command_queue* oclCreateCommandQueue(cl_context, cl_device_id, cl_command_queue_properties)’:
/home/hari/cas-offinder/oclfunctions.h:131:35: warning: ‘_cl_command_queue* clCreateCommandQueue(cl_context, cl_device_id, cl_command_queue_properties, cl_int*)’ is deprecated (declared at /opt/AMDAPPSDK-3.0/include/CL/cl.h:1359) [-Wdeprecated-declarations]
  cl_command_queue command_queue = clCreateCommandQueue(context, device, properties, &err);
                                   ^
/home/hari/cas-offinder/oclfunctions.h:131:89: warning: ‘_cl_command_queue* clCreateCommandQueue(cl_context, cl_device_id, cl_command_queue_properties, cl_int*)’ is deprecated (declared at /opt/AMDAPPSDK-3.0/include/CL/cl.h:1359) [-Wdeprecated-declarations]
  cl_command_queue command_queue = clCreateCommandQueue(context, device, properties, &err);
                                                                                         ^
[ 75%] Building CXX object CMakeFiles/cas-offinder.dir/read_fasta.cpp.o
[100%] Building CXX object CMakeFiles/cas-offinder.dir/read_twobit.cpp.o
Linking CXX executable cas-offinder
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `oclCreateBuffer(_cl_context*, unsigned long, unsigned long, void*)':
cas-offinder.cpp:(.text+0x9): undefined reference to `clCreateBuffer'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `oclGetPlatformIDs(unsigned int, _cl_platform_id**, unsigned int*)':
cas-offinder.cpp:(.text+0x42): undefined reference to `clGetPlatformIDs'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `oclGetDeviceIDs(_cl_platform_id*, unsigned long, unsigned int, _cl_device_id**, unsigned int*)':
cas-offinder.cpp:(.text+0x82): undefined reference to `clGetDeviceIDs'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `oclCreateContext(long*, unsigned int, _cl_device_id* const*, void (*)(char const*, void const*, unsigned long, void*), void*)':
cas-offinder.cpp:(.text+0xc9): undefined reference to `clCreateContext'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `oclCreateProgramWithSource(_cl_context*, unsigned int, char const**, unsigned long const*)':
cas-offinder.cpp:(.text+0x109): undefined reference to `clCreateProgramWithSource'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `oclBuildProgram(_cl_program*, unsigned int, _cl_device_id* const*, char const*, void (*)(_cl_program*, void*), void*)':
cas-offinder.cpp:(.text+0x157): undefined reference to `clBuildProgram'
cas-offinder.cpp:(.text+0x1c0): undefined reference to `clGetProgramBuildInfo'
cas-offinder.cpp:(.text+0x1ea): undefined reference to `clGetProgramBuildInfo'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `oclCreateKernel(_cl_program*, char const*)':
cas-offinder.cpp:(.text+0x229): undefined reference to `clCreateKernel'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `oclCreateCommandQueue(_cl_context*, _cl_device_id*, unsigned long)':
cas-offinder.cpp:(.text+0x269): undefined reference to `clCreateCommandQueue'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `oclGetDeviceInfo(_cl_device_id*, unsigned int, unsigned long, void*, unsigned long*)':
cas-offinder.cpp:(.text+0x2a2): undefined reference to `clGetDeviceInfo'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `oclReleaseKernel(_cl_kernel*)':
cas-offinder.cpp:(.text+0x2e7): undefined reference to `clReleaseKernel'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `oclReleaseCommandQueue(_cl_command_queue*)':
cas-offinder.cpp:(.text+0x327): undefined reference to `clReleaseCommandQueue'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `oclReleaseContext(_cl_context*)':
cas-offinder.cpp:(.text+0x367): undefined reference to `clReleaseContext'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `oclEnqueueWriteBuffer(_cl_command_queue*, _cl_mem*, unsigned int, unsigned long, unsigned long, void const*, unsigned int, _cl_event* const*, _cl_event**)':
cas-offinder.cpp:(.text+0x3c1): undefined reference to `clEnqueueWriteBuffer'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `oclFinish(_cl_command_queue*)':
cas-offinder.cpp:(.text+0x402): undefined reference to `clFinish'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `oclSetKernelArg(_cl_kernel*, unsigned int, unsigned long, void const*)':
cas-offinder.cpp:(.text+0x442): undefined reference to `clSetKernelArg'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `oclEnqueueNDRangeKernel(_cl_command_queue*, _cl_kernel*, unsigned int, unsigned long const*, unsigned long const*, unsigned long const*, unsigned int, _cl_event* const*, _cl_event**)':
cas-offinder.cpp:(.text+0x4a1): undefined reference to `clEnqueueNDRangeKernel'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `oclEnqueueReadBuffer(_cl_command_queue*, _cl_mem*, unsigned int, unsigned long, unsigned long, void*, unsigned int, _cl_event* const*, _cl_event**)':
cas-offinder.cpp:(.text+0x501): undefined reference to `clEnqueueReadBuffer'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `clearbufvec(std::vector<_cl_mem*, std::allocator<_cl_mem*> >*)':
cas-offinder.cpp:(.text+0x572): undefined reference to `clReleaseMemObject'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `Cas_OFFinder::releaseLociinfo()':
cas-offinder.cpp:(.text+0x852): undefined reference to `clReleaseMemObject'
cas-offinder.cpp:(.text+0x8ca): undefined reference to `clReleaseMemObject'
cas-offinder.cpp:(.text+0x932): undefined reference to `clReleaseMemObject'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `Cas_OFFinder::compareAll(char const*)':
cas-offinder.cpp:(.text+0xe8d): undefined reference to `clEnqueueWriteBuffer'
cas-offinder.cpp:(.text+0xeda): undefined reference to `clEnqueueWriteBuffer'
cas-offinder.cpp:(.text+0xf25): undefined reference to `clEnqueueWriteBuffer'
cas-offinder.cpp:(.text+0xf3a): undefined reference to `clFinish'
cas-offinder.cpp:(.text+0xf66): undefined reference to `clSetKernelArg'
cas-offinder.cpp:(.text+0xfc4): undefined reference to `clEnqueueNDRangeKernel'
cas-offinder.cpp:(.text+0x1172): undefined reference to `clFinish'
cas-offinder.cpp:(.text+0x11c3): undefined reference to `clEnqueueReadBuffer'
cas-offinder.cpp:(.text+0x122a): undefined reference to `clEnqueueReadBuffer'
cas-offinder.cpp:(.text+0x127d): undefined reference to `clEnqueueReadBuffer'
cas-offinder.cpp:(.text+0x12d4): undefined reference to `clEnqueueReadBuffer'
cas-offinder.cpp:(.text+0x12ec): undefined reference to `clFinish'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `Cas_OFFinder::init_platforms()':
cas-offinder.cpp:(.text+0x19d1): undefined reference to `clGetPlatformIDs'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `Cas_OFFinder::print_usage()':
cas-offinder.cpp:(.text+0x1fb4): undefined reference to `clGetDeviceIDs'
cas-offinder.cpp:(.text+0x2021): undefined reference to `clGetDeviceInfo'
cas-offinder.cpp:(.text+0x20fb): undefined reference to `clGetDeviceIDs'
cas-offinder.cpp:(.text+0x2169): undefined reference to `clGetDeviceInfo'
cas-offinder.cpp:(.text+0x2241): undefined reference to `clGetDeviceIDs'
cas-offinder.cpp:(.text+0x22b1): undefined reference to `clGetDeviceInfo'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `Cas_OFFinder::~Cas_OFFinder()':
cas-offinder.cpp:(.text+0x25fa): undefined reference to `clReleaseKernel'
cas-offinder.cpp:(.text+0x265a): undefined reference to `clReleaseKernel'
cas-offinder.cpp:(.text+0x26b1): undefined reference to `clReleaseCommandQueue'
cas-offinder.cpp:(.text+0x26ce): undefined reference to `clReleaseContext'
cas-offinder.cpp:(.text+0x271a): undefined reference to `clReleaseMemObject'
cas-offinder.cpp:(.text+0x2782): undefined reference to `clReleaseMemObject'
cas-offinder.cpp:(.text+0x27ea): undefined reference to `clReleaseMemObject'
cas-offinder.cpp:(.text+0x2852): undefined reference to `clReleaseMemObject'
cas-offinder.cpp:(.text+0x28ba): undefined reference to `clReleaseMemObject'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `Cas_OFFinder::initOpenCL()':
cas-offinder.cpp:(.text+0x327d): undefined reference to `clGetDeviceIDs'
cas-offinder.cpp:(.text+0x32f1): undefined reference to `clCreateKernel'
cas-offinder.cpp:(.text+0x3346): undefined reference to `clCreateKernel'
cas-offinder.cpp:(.text+0x33aa): undefined reference to `clCreateCommandQueue'
cas-offinder.cpp:(.text+0x3428): undefined reference to `clGetDeviceInfo'
cas-offinder.cpp:(.text+0x3468): undefined reference to `clCreateContext'
cas-offinder.cpp:(.text+0x34c2): undefined reference to `clCreateProgramWithSource'
cas-offinder.cpp:(.text+0x34ec): undefined reference to `clBuildProgram'
cas-offinder.cpp:(.text+0x3510): undefined reference to `clCreateKernel'
cas-offinder.cpp:(.text+0x37be): undefined reference to `clGetProgramBuildInfo'
cas-offinder.cpp:(.text+0x37e9): undefined reference to `clGetProgramBuildInfo'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `Cas_OFFinder::setChrData()':
cas-offinder.cpp:(.text+0x3f0a): undefined reference to `clReleaseMemObject'
cas-offinder.cpp:(.text+0x3f7a): undefined reference to `clReleaseMemObject'
cas-offinder.cpp:(.text+0x3fea): undefined reference to `clReleaseMemObject'
cas-offinder.cpp:(.text+0x408d): undefined reference to `clCreateBuffer'
cas-offinder.cpp:(.text+0x40f8): undefined reference to `clCreateBuffer'
cas-offinder.cpp:(.text+0x415c): undefined reference to `clSetKernelArg'
cas-offinder.cpp:(.text+0x418a): undefined reference to `clSetKernelArg'
cas-offinder.cpp:(.text+0x41b8): undefined reference to `clSetKernelArg'
cas-offinder.cpp:(.text+0x41e3): undefined reference to `clSetKernelArg'
cas-offinder.cpp:(.text+0x4211): undefined reference to `clSetKernelArg'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o:cas-offinder.cpp:(.text+0x423f): more undefined references to `clSetKernelArg' follow
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `Cas_OFFinder::setChrData()':
cas-offinder.cpp:(.text+0x4311): undefined reference to `clCreateBuffer'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `Cas_OFFinder::loadNextChunk()':
cas-offinder.cpp:(.text+0x45db): undefined reference to `clEnqueueWriteBuffer'
cas-offinder.cpp:(.text+0x468e): undefined reference to `clEnqueueWriteBuffer'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `Cas_OFFinder::findPattern()':
cas-offinder.cpp:(.text+0x4851): undefined reference to `clEnqueueWriteBuffer'
cas-offinder.cpp:(.text+0x489c): undefined reference to `clEnqueueNDRangeKernel'
cas-offinder.cpp:(.text+0x498f): undefined reference to `clEnqueueReadBuffer'
cas-offinder.cpp:(.text+0x4ab0): undefined reference to `clCreateBuffer'
cas-offinder.cpp:(.text+0x4b1b): undefined reference to `clCreateBuffer'
cas-offinder.cpp:(.text+0x4b85): undefined reference to `clCreateBuffer'
cas-offinder.cpp:(.text+0x4bec): undefined reference to `clSetKernelArg'
cas-offinder.cpp:(.text+0x4c1a): undefined reference to `clSetKernelArg'
cas-offinder.cpp:(.text+0x4c48): undefined reference to `clSetKernelArg'
cas-offinder.cpp:(.text+0x4c7a): undefined reference to `clFinish'
cas-offinder.cpp:(.text+0x4cfd): undefined reference to `clEnqueueReadBuffer'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `Cas_OFFinder::readInputFile(char const*)':
cas-offinder.cpp:(.text+0x6214): undefined reference to `clCreateBuffer'
cas-offinder.cpp:(.text+0x62a0): undefined reference to `clEnqueueWriteBuffer'
cas-offinder.cpp:(.text+0x62f0): undefined reference to `clEnqueueWriteBuffer'
cas-offinder.cpp:(.text+0x631d): undefined reference to `clCreateBuffer'
cas-offinder.cpp:(.text+0x638b): undefined reference to `clCreateBuffer'
cas-offinder.cpp:(.text+0x63f7): undefined reference to `clCreateBuffer'
cas-offinder.cpp:(.text+0x6482): undefined reference to `clEnqueueWriteBuffer'
cas-offinder.cpp:(.text+0x649a): undefined reference to `clFinish'
cas-offinder.cpp:(.text+0x64c9): undefined reference to `clSetKernelArg'
cas-offinder.cpp:(.text+0x64f8): undefined reference to `clSetKernelArg'
cas-offinder.cpp:(.text+0x6527): undefined reference to `clSetKernelArg'
cas-offinder.cpp:(.text+0x6556): undefined reference to `clSetKernelArg'
cas-offinder.cpp:(.text+0x6585): undefined reference to `clSetKernelArg'
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o:cas-offinder.cpp:(.text+0x65b4): more undefined references to `clSetKernelArg' follow
CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function `Cas_OFFinder::readInputFile(char const*)':
cas-offinder.cpp:(.text+0x670b): undefined reference to `clCreateBuffer'
collect2: error: ld returned 1 exit status
make[2]: *** [cas-offinder] Error 1
make[1]: *** [CMakeFiles/cas-offinder.dir/all] Error 2
make: *** [all] Error 2

I have tried to add the include library to my LD_LIBRARY_PATH but still dont get it to compile. Please can you help with with what may be a specific issue with the way my GPU drivers are setup. I am running Catalyst on Ubuntu 14.04 with AMD Radeon dual HD 7870.

hari@hjubuntu:~/cas-offinder$ fglrxinfo 
display: :0  screen: 0
OpenGL vendor string: Advanced Micro Devices, Inc.
OpenGL renderer string: AMD Radeon HD 7800 Series 
OpenGL version string: 4.5.13399 Compatibility Profile Context 15.201.1151

ii  fglrx-updates                                         2:15.201-0ubuntu0.14.04.1                           amd64        Video driver for the AMD graphics accelerators
ii  fglrx-updates-core                                    2:15.201-0ubuntu0.14.04.1                           amd64        Minimal video driver for the AMD graphics accelerators

[pjb7687]

Dear Hari,

It looks like your OpenCL library is corrupted, please download the most recent version of AMD APP SDK and try again. Maybe you need to specify the installation path of APP SDK when you configure Cas-OFFinder by CMake.

Best, Jeongbin

On Sun, Mar 6, 2016 at 6:34 PM, Hari Jayaram notifications@github.com wrote:

Hello, Sorry to email this in as an issue but I am having some issues getting cas-offinder running on my system.

When I try the binary is get the message:

hari@hjubuntu:~/cas-offinder$ ./cas-offinder clGetPlatformIDs Failed: -1001

When I tried compiling I get the message:

cmake -DOPENCL_INCLUDE_DIRS=/opt/AMDAPPSDK-3.0/include -DOPENCL_LIBRARIES=/opt/AMDAPPSDK-3.0/lib/x86_64/libOpenCL.so .

hari@hjubuntu:~/cas-offinder$ make Scanning dependencies of target cas-offinder [ 25%] Building CXX object CMakeFiles/cas-offinder.dir/main.cpp.o [ 50%] Building CXX object CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o In file included from /home/hari/cas-offinder/cas-offinder.cpp:4:0: /home/hari/cas-offinder/oclfunctions.h: In function ‘_cl_command_queue* oclCreateCommandQueue(cl_context, cl_device_id, cl_command_queue_properties)’: /home/hari/cas-offinder/oclfunctions.h:131:35: warning: ‘_cl_command_queue* clCreateCommandQueue(cl_context, cl_device_id, cl_command_queue_properties, clint)’ is deprecated (declared at /opt/AMDAPPSDK-3.0/include/CL/cl.h:1359) [-Wdeprecated-declarations] cl_command_queue command_queue = clCreateCommandQueue(context, device, properties, &err); ^ /home/hari/cas-offinder/oclfunctions.h:131:89: warning: ‘_cl_commandqueue clCreateCommandQueue(cl_context, cl_device_id, cl_command_queue_properties, clint)’ is deprecated (declared at /opt/AMDAPPSDK-3.0/include/CL/cl.h:1359) [-Wdeprecated-declarations] cl_command_queue command_queue = clCreateCommandQueue(context, device, properties, &err); ^ [ 75%] Building CXX object CMakeFiles/cas-offinder.dir/read_fasta.cpp.o [100%] Building CXX object CMakeFiles/cas-offinder.dir/read_twobit.cpp.o Linking CXX executable cas-offinder CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function oclCreateBuffer(_cl_context_, unsigned long, unsigned long, void_)': cas-offinder.cpp:(.text+0x9): undefined reference toclCreateBuffer' CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In functionoclGetPlatformIDs(unsigned int, _cl_platform_id__, unsigned int_)': cas-offinder.cpp:(.text+0x42): undefined reference toclGetPlatformIDs' CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In functionoclGetDeviceIDs(_cl_platform_id_, unsigned long, unsigned int, _cl_device_id__, unsigned int_)': cas-offinder.cpp:(.text+0x82): undefined reference toclGetDeviceIDs' CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In functionoclCreateContext(long_, unsigned int, _cl_device_id_ const_, void (_)(char const_, void const_, unsigned long, void_), void_)': cas-offinder.cpp:(.text+0xc9): undefined reference toclCreateContext' CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In functionoclCreateProgramWithSource(_cl_context_, unsigned int, char const__, unsigned long const_)': cas-offinder.cpp:(.text+0x109): undefined reference toclCreateProgramWithSource' CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In functionoclBuildProgram(_cl_program_, unsigned int, _cl_device_id_ const_, char const_, void (_)(_cl_program_, void_), void_)': cas-offinder.cpp:(.text+0x157): undefined reference toclBuildProgram' cas-offinder.cpp:(.text+0x1c0): undefined reference toclGetProgramBuildInfo' cas-offinder.cpp:(.text+0x1ea): undefined reference toclGetProgramBuildInfo' CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In functionoclCreateKernel(_cl_program_, char const_)': cas-offinder.cpp:(.text+0x229): undefined reference toclCreateKernel' CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In functionoclCreateCommandQueue(_cl_context_, _cl_device_id_, unsigned long)': cas-offinder.cpp:(.text+0x269): undefined reference toclCreateCommandQueue' CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In functionoclGetDeviceInfo(_cl_device_id_, unsigned int, unsigned long, void_, unsigned long_)': cas-offinder.cpp:(.text+0x2a2): undefined reference toclGetDeviceInfo' CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In functionoclReleaseKernel(_cl_kernel_)': cas-offinder.cpp:(.text+0x2e7): undefined reference toclReleaseKernel' CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In functionoclReleaseCommandQueue(_cl_command_queue_)': cas-offinder.cpp:(.text+0x327): undefined reference toclReleaseCommandQueue' CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In functionoclReleaseContext(_cl_context_)': cas-offinder.cpp:(.text+0x367): undefined reference toclReleaseContext' CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In functionoclEnqueueWriteBuffer(_cl_command_queue_, _cl_mem_, unsigned int, unsigned long, unsigned long, void const_, unsigned int, _cl_event_ const_, _cl_event__)': cas-offinder.cpp:(.text+0x3c1): undefined reference toclEnqueueWriteBuffer' CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In functionoclFinish(_cl_command_queue_)': cas-offinder.cpp:(.text+0x402): undefined reference toclFinish' CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In functionoclSetKernelArg(_cl_kernel_, unsigned int, unsigned long, void const_)': cas-offinder.cpp:(.text+0x442): undefined reference toclSetKernelArg' CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In functionoclEnqueueNDRangeKernel(_cl_command_queue_, _cl_kernel_, unsigned int, unsigned long const_, unsigned long const_, unsigned long const_, unsigned int, _cl_event_ const_, _cl_event__)': cas-offinder.cpp:(.text+0x4a1): undefined reference toclEnqueueNDRangeKernel' CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In functionoclEnqueueReadBuffer(_cl_command_queue_, _cl_mem_, unsigned int, unsigned long, unsigned long, void_, unsigned int, _cl_event\* const_, _cl_event__)': cas-offinder.cpp:(.text+0x501): undefined reference toclEnqueueReadBuffer' CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In functionclearbufvec(std::vector<_cl_mem_, std::allocator<_cl_mem_> >_)': cas-offinder.cpp:(.text+0x572): undefined reference toclReleaseMemObject' CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In functionCas_OFFinder::releaseLociinfo()': cas-offinder.cpp:(.text+0x852): undefined reference toclReleaseMemObject' cas-offinder.cpp:(.text+0x8ca): undefined reference toclReleaseMemObject' cas-offinder.cpp:(.text+0x932): undefined reference toclReleaseMemObject' CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In functionCas_OFFinder::compareAll(char const_)': cas-offinder.cpp:(.text+0xe8d): undefined reference toclEnqueueWriteBuffer' cas-offinder.cpp:(.text+0xeda): undefined reference toclEnqueueWriteBuffer' cas-offinder.cpp:(.text+0xf25): undefined reference toclEnqueueWriteBuffer' cas-offinder.cpp:(.text+0xf3a): undefined reference toclFinish' cas-offinder.cpp:(.text+0xf66): undefined reference toclSetKernelArg' cas-offinder.cpp:(.text+0xfc4): undefined reference toclEnqueueNDRangeKernel' cas-offinder.cpp:(.text+0x1172): undefined reference toclFinish' cas-offinder.cpp:(.text+0x11c3): undefined reference toclEnqueueReadBuffer' cas-offinder.cpp:(.text+0x122a): undefined reference toclEnqueueReadBuffer' cas-offinder.cpp:(.text+0x127d): undefined reference toclEnqueueReadBuffer' cas-offinder.cpp:(.text+0x12d4): undefined reference toclEnqueueReadBuffer' cas-offinder.cpp:(.text+0x12ec): undefined reference toclFinish' CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In functionCas_OFFinder::init_platforms()': cas-offinder.cpp:(.text+0x19d1): undefined reference toclGetPlatformIDs' CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In functionCas_OFFinder::print_usage()': cas-offinder.cpp:(.text+0x1fb4): undefined reference toclGetDeviceIDs' cas-offinder.cpp:(.text+0x2021): undefined reference toclGetDeviceInfo' cas-offinder.cpp:(.text+0x20fb): undefined reference toclGetDeviceIDs' cas-offinder.cpp:(.text+0x2169): undefined reference toclGetDeviceInfo' cas-offinder.cpp:(.text+0x2241): undefined reference toclGetDeviceIDs' cas-offinder.cpp:(.text+0x22b1): undefined reference toclGetDeviceInfo' CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In functionCas_OFFinder::~Cas_OFFinder()': cas-offinder.cpp:(.text+0x25fa): undefined reference toclReleaseKernel' cas-offinder.cpp:(.text+0x265a): undefined reference toclReleaseKernel' cas-offinder.cpp:(.text+0x26b1): undefined reference toclReleaseCommandQueue' cas-offinder.cpp:(.text+0x26ce): undefined reference toclReleaseContext' cas-offinder.cpp:(.text+0x271a): undefined reference toclReleaseMemObject' cas-offinder.cpp:(.text+0x2782): undefined reference toclReleaseMemObject' cas-offinder.cpp:(.text+0x27ea): undefined reference toclReleaseMemObject' cas-offinder.cpp:(.text+0x2852): undefined reference toclReleaseMemObject' cas-offinder.cpp:(.text+0x28ba): undefined reference toclReleaseMemObject' CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In functionCas_OFFinder::initOpenCL()': cas-offinder.cpp:(.text+0x327d): undefined reference toclGetDeviceIDs' cas-offinder.cpp:(.text+0x32f1): undefined reference toclCreateKernel' cas-offinder.cpp:(.text+0x3346): undefined reference toclCreateKernel' cas-offinder.cpp:(.text+0x33aa): undefined reference toclCreateCommandQueue' cas-offinder.cpp:(.text+0x3428): undefined reference toclGetDeviceInfo' cas-offinder.cpp:(.text+0x3468): undefined reference toclCreateContext' cas-offinder.cpp:(.text+0x34c2): undefined reference toclCreateProgramWithSource' cas-offinder.cpp:(.text+0x34ec): undefined reference toclBuildProgram' cas-offinder.cpp:(.text+0x3510): undefined reference toclCreateKernel' cas-offinder.cpp:(.text+0x37be): undefined reference toclGetProgramBuildInfo' cas-offinder.cpp:(.text+0x37e9): undefined reference toclGetProgramBuildInfo' CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In functionCas_OFFinder::setChrData()': cas-offinder.cpp:(.text+0x3f0a): undefined reference toclReleaseMemObject' cas-offinder.cpp:(.text+0x3f7a): undefined reference toclReleaseMemObject' cas-offinder.cpp:(.text+0x3fea): undefined reference toclReleaseMemObject' cas-offinder.cpp:(.text+0x408d): undefined reference toclCreateBuffer' cas-offinder.cpp:(.text+0x40f8): undefined reference toclCreateBuffer' cas-offinder.cpp:(.text+0x415c): undefined reference toclSetKernelArg' cas-offinder.cpp:(.text+0x418a): undefined reference toclSetKernelArg' cas-offinder.cpp:(.text+0x41b8): undefined reference toclSetKernelArg' cas-offinder.cpp:(.text+0x41e3): undefined reference toclSetKernelArg' cas-offinder.cpp:(.text+0x4211): undefined reference toclSetKernelArg' CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o:cas-offinder.cpp:(.text+0x423f): more undefined references toclSetKernelArg' follow CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In functionCas_OFFinder::setChrData()': cas-offinder.cpp:(.text+0x4311): undefined reference toclCreateBuffer' CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In functionCas_OFFinder::loadNextChunk()': cas-offinder.cpp:(.text+0x45db): undefined reference toclEnqueueWriteBuffer' cas-offinder.cpp:(.text+0x468e): undefined reference toclEnqueueWriteBuffer' CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In functionCas_OFFinder::findPattern()': cas-offinder.cpp:(.text+0x4851): undefined reference toclEnqueueWriteBuffer' cas-offinder.cpp:(.text+0x489c): undefined reference toclEnqueueNDRangeKernel' cas-offinder.cpp:(.text+0x498f): undefined reference toclEnqueueReadBuffer' cas-offinder.cpp:(.text+0x4ab0): undefined reference toclCreateBuffer' cas-offinder.cpp:(.text+0x4b1b): undefined reference toclCreateBuffer' cas-offinder.cpp:(.text+0x4b85): undefined reference toclCreateBuffer' cas-offinder.cpp:(.text+0x4bec): undefined reference toclSetKernelArg' cas-offinder.cpp:(.text+0x4c1a): undefined reference toclSetKernelArg' cas-offinder.cpp:(.text+0x4c48): undefined reference toclSetKernelArg' cas-offinder.cpp:(.text+0x4c7a): undefined reference toclFinish' cas-offinder.cpp:(.text+0x4cfd): undefined reference toclEnqueueReadBuffer' CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In functionCasOFFinder::readInputFile(char const)': cas-offinder.cpp:(.text+0x6214): undefined reference to clCreateBuffer' cas-offinder.cpp:(.text+0x62a0): undefined reference toclEnqueueWriteBuffer' cas-offinder.cpp:(.text+0x62f0): undefined reference to clEnqueueWriteBuffer' cas-offinder.cpp:(.text+0x631d): undefined reference toclCreateBuffer' cas-offinder.cpp:(.text+0x638b): undefined reference to clCreateBuffer' cas-offinder.cpp:(.text+0x63f7): undefined reference toclCreateBuffer' cas-offinder.cpp:(.text+0x6482): undefined reference to clEnqueueWriteBuffer' cas-offinder.cpp:(.text+0x649a): undefined reference toclFinish' cas-offinder.cpp:(.text+0x64c9): undefined reference to clSetKernelArg' cas-offinder.cpp:(.text+0x64f8): undefined reference toclSetKernelArg' cas-offinder.cpp:(.text+0x6527): undefined reference to clSetKernelArg' cas-offinder.cpp:(.text+0x6556): undefined reference toclSetKernelArg' cas-offinder.cpp:(.text+0x6585): undefined reference to clSetKernelArg' CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o:cas-offinder.cpp:(.text+0x65b4): more undefined references toclSetKernelArg' follow CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o: In function Cas_OFFinder::readInputFile(char const*)': cas-offinder.cpp:(.text+0x670b): undefined reference toclCreateBuffer' collect2: error: ld returned 1 exit status make[2]: * [cas-offinder] Error 1 make[1]: * [CMakeFiles/cas-offinder.dir/all] Error 2 make: *\ [all] Error 2

I have tried to add the include library to my LD_LIBRARY_PATH but still dont get it to compile. Please can yo help with with what may be a specific issue with the way my GPU drivers are setup. I am running Catalyst

hari@hjubuntu:~/cas-offinder$ fglrxinfo display: :0 screen: 0 OpenGL vendor string: Advanced Micro Devices, Inc. OpenGL renderer string: AMD Radeon HD 7800 Series OpenGL version string: 4.5.13399 Compatibility Profile Context 15.201.1151

ii fglrx-updates 2:15.201-0ubuntu0.14.04.1 amd64 Video driver for the AMD graphics accelerators ii fglrx-updates-core 2:15.201-0ubuntu0.14.04.1 amd64 Minimal video driver for the AMD graphics accelerators

— Reply to this email directly or view it on GitHub https://github.com/snugel/cas-offinder/issues/4.

[harijay]

Thanks for your help Jeongbin. I have it working now. I removed all the Ubuntu supplied fglrx drivers in 14.04 I downloaded the Ubuntu/Trusty run script that creates the deb files from AMD site This was called the : AMD OpenCL™ 2.0 Driver

Unlike the Ubuntu supllied fglrx driver and fglrx-updates drivers. The drivers installed using this deb file worked perfectly.

sudo dpkg --install fglrx_14.410-0ubuntu1_amd64.deb
sudo dpkg --install fglrx-dev_14.410-0ubuntu1_amd64.deb
sudo dpkg --instal fglrx-amdcccle_14.410-0ubuntu1_amd64.deb
sudo ati-config --adapter=all --initial

Once I rebooted. The binary downloaded from your site worked perfectly

I was also able to compile the cloned repository and it even used the includes files from /opt/AMDAPPSDK-3.0

hari@hjubuntu:~/cas-offinder$git clone https://github.com/snugel/cas-offinder.git
hari@hjubuntu:~/cas-offinder$ cmake .
-- The C compiler identification is GNU 4.8.4
-- The CXX compiler identification is GNU 4.8.4
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Found OpenCL library: /usr/lib/libOpenCL.so
Found OpenCL library at /opt/AMDAPPSDK-3.0.
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp  
-- Configuring done
-- Generating done
-- Build files have been written to: /home/hari/cas-offinder
hari@hjubuntu:~/cas-offinder$ make
Scanning dependencies of target cas-offinder
[ 25%] Building CXX object CMakeFiles/cas-offinder.dir/main.cpp.o
[ 50%] Building CXX object CMakeFiles/cas-offinder.dir/cas-offinder.cpp.o
In file included from /home/hari/cas-offinder/cas-offinder.cpp:4:0:
/home/hari/cas-offinder/oclfunctions.h: In function ‘_cl_command_queue* oclCreateCommandQueue(cl_context, cl_device_id, cl_command_queue_properties)’:
/home/hari/cas-offinder/oclfunctions.h:131:35: warning: ‘_cl_command_queue* clCreateCommandQueue(cl_context, cl_device_id, cl_command_queue_properties, cl_int*)’ is deprecated (declared at /opt/AMDAPPSDK-3.0/include/CL/cl.h:1359) [-Wdeprecated-declarations]
  cl_command_queue command_queue = clCreateCommandQueue(context, device, properties, &err);
                                   ^
/home/hari/cas-offinder/oclfunctions.h:131:89: warning: ‘_cl_command_queue* clCreateCommandQueue(cl_context, cl_device_id, cl_command_queue_properties, cl_int*)’ is deprecated (declared at /opt/AMDAPPSDK-3.0/include/CL/cl.h:1359) [-Wdeprecated-declarations]
  cl_command_queue command_queue = clCreateCommandQueue(context, device, properties, &err);
                                                                                         ^
[ 75%] Building CXX object CMakeFiles/cas-offinder.dir/read_fasta.cpp.o
[100%] Building CXX object CMakeFiles/cas-offinder.dir/read_twobit.cpp.o
Linking CXX executable cas-offinder
[100%] Built target cas-offinder

This worked perfectly Thank you for your help