Question about installation of PFAC library

Accelerated Computing GPU-Accelerated Libraries
1

Dear all,

I am trying to achieve high-speed DNA sequence data anlaysis using our original algorithm, and consider that cuda and PFAC library should be useful for this trial.
I have a machine with Tesla K20c, where ubuntu and CUDA-7.0 is already installed. I downloaded the package from GitHub - pfac-lib/PFAC: PFAC is an open library for exact string matching performed on NVIDIA GPUs, and try make in directory PFAC. To solve compile errors occured in the first trial, I modified common.mk and src/Makefile as follows:

%diff common.mk common.mk~
63,64c63,64
< sm_21_support := $(if $(filter $(nvcc_version), 3.2 4.0 4.1 4.2 7.0),1,)
< sm_30_support := $(if $(filter $(nvcc_version), 4.2 7.0),1,)

sm_21_support := $(if $(filter $(nvcc_version), 3.2 4.0 4.1 4.2),1,)
sm_30_support := $(if $(filter $(nvcc_version), 4.2),1,)
% diff Makefile~ Makefile
51,53c51,53
< #cu_cpp_sm13_loc = $(patsubst %.cpp,$(OBJ_DIR)/sm13_%.cpp,$(CU_CPP))
< #cu_cpp_sm12_loc = $(patsubst %.cpp,$(OBJ_DIR)/sm12_%.cpp,$(CU_CPP))
< #cu_cpp_sm11_loc = $(patsubst %.cpp,$(OBJ_DIR)/sm11_%.cpp,$(CU_CPP))

cu_cpp_sm13_loc = $(patsubst %.cpp,$(OBJ_DIR)/sm13_%.cpp,$(CU_CPP))
cu_cpp_sm12_loc = $(patsubst %.cpp,$(OBJ_DIR)/sm12_%.cpp,$(CU_CPP))
cu_cpp_sm11_loc = $(patsubst %.cpp,$(OBJ_DIR)/sm11_%.cpp,$(CU_CPP))
58,60c58,60
< #cu_cpp_obj_sm13_loc = $(patsubst %.cpp,$(OBJ_DIR)/sm13_%.cpp.o,$(CU_CPP))
< #cu_cpp_obj_sm12_loc = $(patsubst %.cpp,$(OBJ_DIR)/sm12_%.cpp.o,$(CU_CPP))
< #cu_cpp_obj_sm11_loc = $(patsubst %.cpp,$(OBJ_DIR)/sm11_%.cpp.o,$(CU_CPP))

cu_cpp_obj_sm13_loc = $(patsubst %.cpp,$(OBJ_DIR)/sm13_%.cpp.o,$(CU_CPP))
cu_cpp_obj_sm12_loc = $(patsubst %.cpp,$(OBJ_DIR)/sm12_%.cpp.o,$(CU_CPP))
cu_cpp_obj_sm11_loc = $(patsubst %.cpp,$(OBJ_DIR)/sm11_%.cpp.o,$(CU_CPP))
71,73c71
< mk_libso_no21: $(cu_cpp_sm20_loc)
< $(CXX) -shared -o $(LIB_DIR)/libpfac_sm20.so $(LIBS) $(cu_cpp_obj_sm20_l
oc)
< #mk_libso_no21: $(cu_cpp_sm20_loc) $(cu_cpp_sm13_loc) $(cu_cpp_sm12_loc) $(cu_cpp_sm11_loc)

#mk_libso_no21: $(cu_cpp_sm20_loc)
75,77c73,77
< # $(CXX) -shared -o $(LIB_DIR)/libpfac_sm13.so $(LIBS) $(cu_cpp_obj_sm13_loc)
< # $(CXX) -shared -o $(LIB_DIR)/libpfac_sm12.so $(LIBS) $(cu_cpp_obj_sm12_loc)
< # $(CXX) -shared -o $(LIB_DIR)/libpfac_sm11.so $(LIBS) $(cu_cpp_obj_sm11_loc)

mk_libso_no21: $(cu_cpp_sm20_loc) $(cu_cpp_sm13_loc) $(cu_cpp_sm12_loc) $(cu_cpp_sm11_loc)
$(CXX) -shared -o $(LIB_DIR)/libpfac_sm20.so $(LIBS) $(cu_cpp_obj_sm20_loc)
$(CXX) -shared -o $(LIB_DIR)/libpfac_sm13.so $(LIBS) $(cu_cpp_obj_sm13_loc)
$(CXX) -shared -o $(LIB_DIR)/libpfac_sm12.so $(LIBS) $(cu_cpp_obj_sm12_loc)
$(CXX) -shared -o $(LIB_DIR)/libpfac_sm11.so $(LIBS) $(cu_cpp_obj_sm11_loc)

After retrial of make, the test program enclosed in the archive, named “simple_example.exe” seemed to be successfully generated. However, test run of this program resulted in abort at first assertion.
simple_example.exe: simple_example.cpp:62: int main(int, char**): Assertion `PFAC_STATUS_SUCCESS == PFAC_status’ failed.
I checked by gdb that the value of PFAC_status was PFAC_STATUS_ARCH_MISMATCH when the error occurred.
How can I solve this program?
Thank you for any help.
Koji Doi

2

Your tesla K20c is a cc3.5 device. The PFAC was apparently written to exclusively support only cc1.1, cc1.2, cc1.3, cc2.0, cc2.1 and cc3.0 devices. Take a look in PFAC.cpp (starting at line 153):

cudaDeviceProp deviceProp;
    cudaGetDeviceProperties(&deviceProp, device);

    PFAC_PRINTF("major = %d, minor = %d, name=%s\n", deviceProp.major, deviceProp.minor, deviceProp.name );

    int device_no = 10*deviceProp.major + deviceProp.minor ;
    if ( 30 == device_no ){
        strcpy (modulepath, "libpfac_sm30.so");    
    }else if ( 21 == device_no ){
        strcpy (modulepath, "libpfac_sm21.so");    
    }else if ( 20 == device_no ){
        strcpy (modulepath, "libpfac_sm20.so");
    }else if ( 13 == device_no ){
        strcpy (modulepath, "libpfac_sm13.so");
    }else if ( 12 == device_no ){
        strcpy (modulepath, "libpfac_sm12.so");
    }else if ( 11 == device_no ){
        strcpy (modulepath, "libpfac_sm11.so");
    }else{
        return PFAC_STATUS_ARCH_MISMATCH ;
    }

Your cc3.5 device will put 35 into the above test, and it will fail with PFAC_STATUS_ARCH_MISMATCH

You could try modifying the above test in PFAC.cpp to:

cudaDeviceProp deviceProp;
    cudaGetDeviceProperties(&deviceProp, device);

    PFAC_PRINTF("major = %d, minor = %d, name=%s\n", deviceProp.major, deviceProp.minor, deviceProp.name );

    int device_no = 10*deviceProp.major + deviceProp.minor ;
    if (( 30 == device_no ) || ( 35 == device_no)){ // ****modification here on this line only ****
        strcpy (modulepath, "libpfac_sm30.so");    
    }else if ( 21 == device_no ){
        strcpy (modulepath, "libpfac_sm21.so");    
    }else if ( 20 == device_no ){
        strcpy (modulepath, "libpfac_sm20.so");
    }else if ( 13 == device_no ){
        strcpy (modulepath, "libpfac_sm13.so");
    }else if ( 12 == device_no ){
        strcpy (modulepath, "libpfac_sm12.so");
    }else if ( 11 == device_no ){
        strcpy (modulepath, "libpfac_sm11.so");
    }else{
        return PFAC_STATUS_ARCH_MISMATCH ;
    }

And see what happens, since your cc3.5 device should work fine with a cc3.0 library, but I haven’t actually tested that with this application.

3

Thank you very much, txbob.
I modified PFAC.cpp as suggested, updated all libraries. The problem at the first assertion seems to be solved.

However, simple_example.exe aborts at step 4. the following line.

PFAC_status = PFAC_matchFromHost( handle, h_inputString, input_size, h_matched_result ) ;

PFAC_matchFromHost returns PFAC_STATUS_CUDA_ALLOC_FAILED.
I could not find any information to understand what this error code means and how to solve.
Does anyone have suggestions?

Koji Doi

4

Since CUDA 4.1 the function cudaGetTextureReference() is marked as deprecated.
Link: http://developer.download.nvidia.com/compute/cuda/4_1/rel/toolkit/docs/online/group__CUDART__TEXTURE__DEPRECATED_gc86c8aca553c7d6dcd8c57e5b93882a8.html

The PFAC library use these function in all *.cu kernel files to save transition tables for the state machine in the texture memory of the device. To fix the problem modify all *cu files from:

cudaGetTextureReference( (const struct textureReference**)&texRefTable, "tex_PFAC_table" );

to

cudaGetTextureReference( (const struct textureReference**)&texRefTable, &tex_PFAC_table );

But I have not yet verified the results!

5

Hi there,

I have a question about the installation on Mac OS. I run the installation of PFAC from the github depository.
I have CUDA-6-0 installed and it works well. During the installation with the command “make”, I have the following problem:

g++ -m64 -fopenmp -shared -o ../lib/libpfac_sm20.so -L/<b>Developer/NVIDIA/CUDA-6.0/lib64</b> -lcudart -ldl -lpthread ../obj/sm20_PFAC_kernel.cu.cpp.o ../obj/sm20_PFAC_reduce_kernel.cu.cpp.o ../obj/sm20_PFAC_reduce_inplace_kernel.cu.cpp.o ../obj/sm20_PFAC_kernel_spaceDriven.cu.cpp.o
ld: warning: directory not found for option '-L/Developer/NVIDIA/CUDA-6.0/lib64'
ld: library not found for -lgomp
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[1]: *** [mk_libso_no21] Error 1
make: *** [src] Error 2

The point is, I never had the “lib64” in my CUDA-6-0 directory…

What am I suppose to do? I tried to change my CUDA version. I tried with the 3.2 version mentioned in PFAC documentation, and the 7-5 to check if the “lib64” appears. But nothing.

Any kind of help will be appreciated, and thank you for your time. :)

6

Hi Wocka,
this library use OpenMP to parallelize the CPU version and i think also to use more then one GPU. I don’t use Mac OS but if found something on Stack Overflow that can help you.

Error enabling openmp - “ld: library not found for -lgomp” and Clang errors:
http://stackoverflow.com/questions/20321988/error-enabling-openmp-ld-library-not-found-for-lgomp-and-clang-errors

7

Thank you a lot falCon1394 for this link. I saw this kind of subject, and I will try to go a step forward with your link.

A little question for you, are you using linux? Do you have this folder lib64 with you CUDA version?

8

Yes i am using Linux with the CUDA Version 7.5 and i have this folder. But on Linux there are many symlinks to the real objects in my system.

9

All right. I am trying to install an other GCC compiler version as your link suggested. Then, I will try to install PFAC library again with the other compiler.

Are you using PFAC with this CUDA version? There is no problem with this? Because I read that the 3.2 version of CUDA is the officially tested, right?

Thank you for your advice. :)

10

The original Library doesn’t run on my System (Git master branch). But with the described changes it works on Linux.

Good luck and have fun with the lib!

A little side node for this thread. The authors wrote a subsequent paper to accelerate regular expressions with this library.

Paper name: Accelerating Regular Expression Matching Using Hierarchical Parallel Machines on GPU
http://cial.csie.ncku.edu.tw/st2011/pdf/Accelerating%20Regular%20Expression%20Matching%20Using.pdf

11

Hi Guys,

I know this is a long shot (based on the time), but I seem to have the same error as Kojidoi.

simple_example.exe: simple_example.cpp:62: int main(int, char**): Assertion `PFAC_STATUS_SUCCESS == PFAC_status' failed.

I seem to have a problem with LD_LIBRARY_PATH, where PFAC_LIB_ROOT seem not to be set properly.

I tried

export LD_LIBRARY_PATH=$(PFAC_LIB_ROOT)/lib:$LD_LIBRARY_PATH

This returns an error

I then tried to export

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/alex/PFAC-master/PFAC/lib:/usr/local/cuda-4.0/lib:/usr/local/cuda-7.0/lib:/usr/local/cuda-7.0/lib64:/usr/local/cuda-4.0/lib64

However, when running the simple example again, I have the following error

PFAC_STATUS_LIB_NOT_EXIST: cannot find PFAC library, please check LD_LIBRARY_PATH 
simple_example.exe: simple_example.cpp:63: int main(int, char**): Assertion `PFAC_STATUS_SUCCESS == PFAC_status' failed.
Aborted (core dumped)

As you can see, it can’t find the PFAC Library. I have looked at the manual PFAC/PFAC_userGuide_r1.1.pdf at master · pfac-lib/PFAC · GitHub but I failed to find a solution.

Any advice would be welcome

12

– Sorry double post –