与CUDA加速在自己的code不能使用CHOLMOD [英] Cannot use CHOLMOD with CUDA acceleration in my own code

查看：609 发布时间：2016/8/24 14:09:14 c cuda suitesparse

本文介绍了与CUDA加速在自己的code不能使用CHOLMOD的处理方法，对大家解决问题具有一定的参考价值，需要的朋友们下面随着小编来一起学习吧！

问题描述

我试图使用 CHOLMOD 与 CUDA 加速 SuiteSparse 4.4.4 。我根据用户手册编译它，我可以成功运行 gpu.sh 在演示文件夹，这表明， GPU所做的工作的一部分。然而，当我尝试使用 CHOLMOD 来经营自己的code，我发现GPU的呼叫数量是始终为0。我设置共＆GT; useGPU 1，环境变量 CHOLMOD_USE_GPU 也设置为1。我的Makefile如下所示。库路径是正确的。对我来说任何建议？

其实我应该提到，我只是运行一个简单的测试用例来求解线性方程。

我试了矩阵用友稀疏矩阵集合，但 nvprof 显示没有 CUDA 申请异形。

一些我试过矩阵：

bmw7st_1： HTTP：//www.cise.ufl。教育/科研/稀疏/矩阵/ GHS_psdef / bmw7st_1.html

nd6k：
http://www.cise.ufl.edu/research/sparse /matrices/ND/nd6k.html

nd24k：
http://www.cise.ufl.edu/research/sparse /matrices/ND/nd24k.html

code：

 的#include＆LT;＆stdio.h中GT;
＃包括LT＆;＆time.h中GT;
＃包括LT＆;＆unistd.h中GT;
＃包括LT＆;＆ASSERT.H GT;
＃包括LT＆; SYS / time.h中＆GT;
＃包括cholmod.hINT主要（无效）
{
    timeval结构T1，T2;
    双elapsedTime;    为const char * matFile =../bmw7st_1.mtx;
    FILE * FP = FOPEN（matFile，R）;
    断言（FP！= NULL）;    cholmod_sparse * A;
    cholmod_dense * X，* B;
    cholmod_factor * L;    cholmod_common * C =（cholmod_common *）malloc的（的sizeof（cholmod_common））;
    cholmod_start（C）; / *启动CHOLMOD * /
    C-＆GT; useGPU = 1;
    C-＆GT; supernodal = CHOLMOD_SUPERNODAL;    A = cholmod_read_sparse（FP，C）; / *在矩阵中读* /
    cholmod_print_sparse（A，A，C）; / *打印矩阵* /
    FCLOSE（FP）;    若（a == NULL || A-＆GT; STYPE == 0）/ * A必须是对称的* /
    {
        cholmod_free_sparse（安培; A，C）;
        cholmod_finish（C）;
        返回（0）;
    }    B = cholmod_ones（A-＆GT; nrow，1，A-＆GT;的xtype，C）; / * B =那些（N，1）* /    函数gettimeofday（＆放大器; T1，NULL）;
    L = cholmod_analyze（A，C）; / * *分析/
    cholmod_factorize（A，L，C）; / * *比化/
    X = cholmod_solve（CHOLMOD_A，L，B，C）; / *解决Ax = b的* /
    函数gettimeofday（＆放大器; t2时，NULL）;
    elapsedTime =（t2.tv_sec  -  t1.tv_sec）* 1000.0;
    elapsedTime + =（t2.tv_usec  -  t1.tv_usec）/ 1000.0;
    的printf（时间：％.4f MS \\ N，elapsedTime）;    cholmod_free_factor（安培; L，C）; / *免费矩阵* /
    cholmod_free_sparse（安培; A，C）;
    cholmod_free_dense（安培; X，C）;
    cholmod_free_dense（安培; B，C）;
    cholmod_finish（C）; / *完成CHOLMOD * /
    返回（0）;
}

的Makefile：

  CC = GCCCFLAGS = -g -Wall -O2 \\
-lrt -lgfortran \\
-gdwarf-2LIBS = $（CHOLMOD）/Lib/libcholmod.a \\
$（AMD）/Lib/libamd.a \\
$（COLAMD）/Lib/libcolamd.a \\
$（LAPACK）/liblapack.a \\
$（OPENBLAS）/lib/libopenblas.so \\
$（XERBLA）/libcerbla.a \\
$（METIS）/libmetis.a \\
$（CAMD）/Lib/libcamd.a \\
$（CCOLAMD）/Lib/libccolamd.a \\
$（SUITESPARSE）/SuiteSparse_config/libsuitesparseconfig.a \\
$（CUDART_LIB）\\
$（CUBLAS_LIB）HEADER_DIR = $（CHOLMOD）/纳入
CONFIG_HEADER_DIR = $（SUITESPARSE）/ SuiteSparse_configOBJ_DIR =。BIN_DIR =。INCLUDES = -I $（HEADER_DIR）\\
-I $（CONFIG_HEADER_DIR）SRCS = $（LS壳的* .c）OBJS = $（SRCS：.C =的.o）OBJS_BUILD = $（壳LS $（OBJ_DIR）/ * O）APP = PROGRM = RM -f所有：$（APP）$（APP）：$（OBJS）
        $（CC）$（CFLAGS）-o $（BIN_DIR）/ $（APP）$（OBJS_BUILD）$（LIBS）％的.o：％.C $（HEADER_DIR）/ * H $（CONFIG_HEADER_DIR）/ * H
        $（CC）$（CFLAGS）$（含）-C $＆LT; -o $（OBJ_DIR）/ $ @清洁：
        $（RM）$（OBJS_BUILD）$（APP）

解决方案

参照第7，CHOLMOD UserGuide.pdf的P34附带SuiteSparse 4.4.4：

只有CHOLMOD的长整型版本可以利用GPU加速。

长整型版本由API调用区分像 cholmod_l_start 而不是 cholmod_start 。

通过修改以下程序：

 的#include＆LT;＆stdio.h中GT;
＃包括LT＆;＆time.h中GT;
＃包括LT＆;＆unistd.h中GT;
＃包括LT＆;＆ASSERT.H GT;
＃包括LT＆; SYS / time.h中＆GT;
＃包括cholmod.hINT主要（无效）
{
    timeval结构T1，T2;
    双elapsedTime;    为const char * matFile =../Matrix/nd6k/nd6k.mtx;
    FILE * FP = FOPEN（matFile，R）;
    断言（FP！= NULL）;    cholmod_sparse * A;
    cholmod_dense * X，* B;
    cholmod_factor * L;    cholmod_common * C =（cholmod_common *）malloc的（的sizeof（cholmod_common））;
    cholmod_l_start（C）; / *启动CHOLMOD * /
    C-＆GT; useGPU = 1;
    C-＆GT; supernodal = CHOLMOD_SUPERNODAL;    A = cholmod_l_read_sparse（FP，C）; / *在矩阵中读* /
    cholmod_l_print_sparse（A，A，C）; / *打印矩阵* /
    FCLOSE（FP）;    若（a == NULL || A-＆GT; STYPE == 0）/ * A必须是对称的* /
    {
        cholmod_l_free_sparse（安培; A，C）;
        cholmod_l_finish（C）;
        返回（0）;
    }    B = cholmod_l_ones（A-＆GT; nrow，1，A-＆GT;的xtype，C）; / * B =那些（N，1）* /    函数gettimeofday（＆放大器; T1，NULL）;
    L = cholmod_l_analyze（A，C）; / * *分析/
    cholmod_l_factorize（A，L，C）; / * *比化/
    X = cholmod_l_solve（CHOLMOD_A，L，B，C）; / *解决Ax = b的* /
    函数gettimeofday（＆放大器; t2时，NULL）;
    elapsedTime =（t2.tv_sec  -  t1.tv_sec）* 1000.0;
    elapsedTime + =（t2.tv_usec  -  t1.tv_usec）/ 1000.0;
    的printf（时间：％.4f MS \\ N，elapsedTime）;
    cholmod_l_gpu_stats（C）;
    cholmod_l_free_factor（安培; L，C）; / *免费矩阵* /
    cholmod_l_free_sparse（安培; A，C）;
    cholmod_l_free_dense（安培; X，C）;
    cholmod_l_free_dense（安培; B，C）;
    cholmod_l_finish（C）; / *完成CHOLMOD * /
    返回（0）;
}

我得到这样的输出：

  $ ./prog
CHOLMOD疏：A：18000按18000，NZ 3457658，上。好
时间：14570.3950毫秒CHOLMOD GPU / CPU统计：
SYRK CPU调用888时1.0637e-01
      GPU调用213时8.9194e-02
GEMM CPU调用711时1.1511e-01
      GPU调用213时1.9351e-03
POTRF CPU调用217时3.2180e-02
      GPU调用5次1.5788e-01
TRSM CPU调用217时6.0409e-01
      GPU调用4时5.6943e-02
一次在BLAS：CPU 8.5774e-01 GPU 3.0595e-01总：1.1637e + 00
装配时间0.0000E + 00 0.0000E + 00
$

指示正在使用的GPU。

I am trying to use CHOLMOD with CUDA acceleration in SuiteSparse 4.4.4. I compiled it according to the user guide and I could run gpu.sh under Demo folder successfully, which showed that the GPU was doing part of the work. However, when I tried to run my own code using CHOLMOD, I found that the number of GPU calls was always 0. I do set Common->useGPU to 1, and the environment variable CHOLMOD_USE_GPU is also set to 1. My Makefile is like the following. The library paths are correct. Any suggestion for me?

Actually I should have mentioned that I am just running a simplest test case to solve a linear system.

I tried several matrices from UF Sparse Matrix Collection, but nvprof showed that no CUDA application was profiled.

Some of the matrices I tried:

bmw7st_1: http://www.cise.ufl.edu/research/sparse/matrices/GHS_psdef/bmw7st_1.html

nd6k: http://www.cise.ufl.edu/research/sparse/matrices/ND/nd6k.html

nd24k: http://www.cise.ufl.edu/research/sparse/matrices/ND/nd24k.html

Code:

#include <stdio.h>
#include <time.h>
#include <unistd.h>
#include <assert.h>
#include <sys/time.h>
#include "cholmod.h"

int main (void)
{
    struct timeval t1, t2;
    double elapsedTime;

    const char* matFile = "../bmw7st_1.mtx";
    FILE* fp = fopen(matFile, "r");
    assert(fp != NULL);

    cholmod_sparse *A ;
    cholmod_dense *x, *b;
    cholmod_factor *L ;

    cholmod_common* c = (cholmod_common*)malloc(sizeof(cholmod_common));
    cholmod_start (c) ; /* start CHOLMOD */
    c->useGPU = 1;
    c->supernodal = CHOLMOD_SUPERNODAL;

    A = cholmod_read_sparse (fp, c) ; /* read in a matrix */
    cholmod_print_sparse (A, "A", c) ; /* print the matrix */
    fclose(fp);

    if (A == NULL || A->stype == 0) /* A must be symmetric */
    {
        cholmod_free_sparse (&A, c) ;
        cholmod_finish (c) ;
        return (0) ;
    }

    b = cholmod_ones (A->nrow, 1, A->xtype, c) ; /* b = ones(n,1) */

    gettimeofday(&t1, NULL);
    L = cholmod_analyze (A, c) ; /* analyze */
    cholmod_factorize (A, L, c) ; /* factorize */
    x = cholmod_solve (CHOLMOD_A, L, b, c) ; /* solve Ax=b */
    gettimeofday(&t2, NULL);
    elapsedTime = (t2.tv_sec - t1.tv_sec) * 1000.0;
    elapsedTime += (t2.tv_usec - t1.tv_usec) / 1000.0;
    printf("Time: %.4f ms\n", elapsedTime);

    cholmod_free_factor (&L, c) ; /* free matrices */
    cholmod_free_sparse (&A, c) ;
    cholmod_free_dense (&x, c) ;
    cholmod_free_dense (&b, c) ;
    cholmod_finish (c) ; /* finish CHOLMOD */
    return (0) ;
}

Makefile:

CC = gcc

CFLAGS = -g -Wall -O2 \
-lrt -lgfortran \
-gdwarf-2

LIBS = $(CHOLMOD)/Lib/libcholmod.a \
$(AMD)/Lib/libamd.a \
$(COLAMD)/Lib/libcolamd.a \
$(LAPACK)/liblapack.a \
$(OPENBLAS)/lib/libopenblas.so \
$(XERBLA)/libcerbla.a \
$(METIS)/libmetis.a \
$(CAMD)/Lib/libcamd.a \
$(CCOLAMD)/Lib/libccolamd.a \
$(SUITESPARSE)/SuiteSparse_config/libsuitesparseconfig.a \
$(CUDART_LIB) \
$(CUBLAS_LIB)

HEADER_DIR = $(CHOLMOD)/Include
CONFIG_HEADER_DIR = $(SUITESPARSE)/SuiteSparse_config

OBJ_DIR = .

BIN_DIR = .

INCLUDES = -I$(HEADER_DIR) \
-I$(CONFIG_HEADER_DIR)

SRCS = $(shell ls *.c)

OBJS = $(SRCS:.c=.o)

OBJS_BUILD = $(shell ls $(OBJ_DIR)/*.o)

APP = prog

RM = rm -f

all: $(APP)

$(APP): $(OBJS)
        $(CC) $(CFLAGS) -o $(BIN_DIR)/$(APP) $(OBJS_BUILD) $(LIBS)

%.o: %.c $(HEADER_DIR)/*.h $(CONFIG_HEADER_DIR)/*.h
        $(CC) $(CFLAGS) $(INCLUDES) -c $< -o $(OBJ_DIR)/$@

clean:
        $(RM) $(OBJS_BUILD) $(APP)

解决方案

Referring to section 7, p34 of the CHOLMOD UserGuide.pdf that ships with SuiteSparse 4.4.4:

Only the long integer version of CHOLMOD can leverage GPU acceleration.

The long integer version is distinguished by api calls like cholmod_l_start instead of cholmod_start.

With the following modifications to your program:

#include <stdio.h>
#include <time.h>
#include <unistd.h>
#include <assert.h>
#include <sys/time.h>
#include "cholmod.h"

int main (void)
{
    struct timeval t1, t2;
    double elapsedTime;

    const char* matFile = "../Matrix/nd6k/nd6k.mtx";
    FILE* fp = fopen(matFile, "r");
    assert(fp != NULL);

    cholmod_sparse *A ;
    cholmod_dense *x, *b;
    cholmod_factor *L ;

    cholmod_common* c = (cholmod_common*)malloc(sizeof(cholmod_common));
    cholmod_l_start (c) ; /* start CHOLMOD */
    c->useGPU = 1;
    c->supernodal = CHOLMOD_SUPERNODAL;

    A = cholmod_l_read_sparse (fp, c) ; /* read in a matrix */
    cholmod_l_print_sparse (A, "A", c) ; /* print the matrix */
    fclose(fp);

    if (A == NULL || A->stype == 0) /* A must be symmetric */
    {
        cholmod_l_free_sparse (&A, c) ;
        cholmod_l_finish (c) ;
        return (0) ;
    }

    b = cholmod_l_ones (A->nrow, 1, A->xtype, c) ; /* b = ones(n,1) */

    gettimeofday(&t1, NULL);
    L = cholmod_l_analyze (A, c) ; /* analyze */
    cholmod_l_factorize (A, L, c) ; /* factorize */
    x = cholmod_l_solve (CHOLMOD_A, L, b, c) ; /* solve Ax=b */
    gettimeofday(&t2, NULL);
    elapsedTime = (t2.tv_sec - t1.tv_sec) * 1000.0;
    elapsedTime += (t2.tv_usec - t1.tv_usec) / 1000.0;
    printf("Time: %.4f ms\n", elapsedTime);
    cholmod_l_gpu_stats(c);
    cholmod_l_free_factor (&L, c) ; /* free matrices */
    cholmod_l_free_sparse (&A, c) ;
    cholmod_l_free_dense (&x, c) ;
    cholmod_l_free_dense (&b, c) ;
    cholmod_l_finish (c) ; /* finish CHOLMOD */
    return (0) ;
}

I get output like this:

$ ./prog
CHOLMOD sparse:  A:  18000-by-18000, nz 3457658, upper.  OK
Time: 14570.3950 ms

CHOLMOD GPU/CPU statistics:
SYRK  CPU calls          888 time   1.0637e-01
      GPU calls          213 time   8.9194e-02
GEMM  CPU calls          711 time   1.1511e-01
      GPU calls          213 time   1.9351e-03
POTRF CPU calls          217 time   3.2180e-02
      GPU calls            5 time   1.5788e-01
TRSM  CPU calls          217 time   6.0409e-01
      GPU calls            4 time   5.6943e-02
time in the BLAS: CPU   8.5774e-01 GPU   3.0595e-01 total:   1.1637e+00
assembly time   0.0000e+00    0.0000e+00
$

indicating the GPU is being used.

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