MPI 程序运行时错误 MPI_GATHER，qsub mpijobparallel
MPI program runtime error MPI_GATHER, qsub mpijobparallel
我正在尝试运行这个快速傅里叶实现代码。它编译正常，但在 运行 时出现此错误。我不知道错误或它的含义。谁能帮我吗？
我通过以下方式编译并 运行 程序：
mpicc -o exec test.c
./exec
代码：
这是我在 GITHUB 上找到的代码。它是快速傅里叶算法的并行版本。
#include <stdio.h>
#include <mpi.h> //To use MPI
#include <complex.h> //to use complex numbers
#include <math.h> //for cos() and sin()
#include "timer.h" //to use timer
#define PI 3.14159265
#define bigN 16384 //Problem Size
#define howmanytimesavg 3
int main()
{
int my_rank,comm_sz;
MPI_Init(NULL,NULL); //start MPI
MPI_Comm_size(MPI_COMM_WORLD,&comm_sz); ///how many processes are we
using?
MPI_Comm_rank(MPI_COMM_WORLD,&my_rank); //which process is this?
double start,finish;
double avgtime = 0;
FILE *outfile;
int h;
if(my_rank == 0) //if process 0 open outfile
{
outfile = fopen("ParallelVersionOutput.txt", "w"); //open from current
directory
}
for(h = 0; h < howmanytimesavg; h++) //loop to run multiple times for AVG
time.
{
if(my_rank == 0) //If it's process 0 starts timer
{
start = MPI_Wtime();
}
int i,k,n,j; //Basic loop variables
double complex evenpart[(bigN / comm_sz / 2)]; //array to save the data
for EVENHALF
double complex oddpart[(bigN / comm_sz / 2)]; //array to save the data
for ODDHALF
double complex evenpartmaster[ (bigN / comm_sz / 2) * comm_sz]; //array
to save the data for EVENHALF
double complex oddpartmaster[ (bigN / comm_sz / 2) * comm_sz]; //array
to save the data for ODDHALF
double storeKsumreal[bigN]; //store the K real variable so we can abuse
symmerty
double storeKsumimag[bigN]; //store the K imaginary variable so we can
abuse symmerty
double subtable[(bigN / comm_sz)][3]; //Each process owns a subtable
from the table below
double table[bigN][3] = //TABLE of numbers to use
{
0,3.6,2.6, //n, Real,Imaginary CREATES TABLE
1,2.9,6.3,
2,5.6,4.0,
3,4.8,9.1,
4,3.3,0.4,
5,5.9,4.8,
6,5.0,2.6,
7,4.3,4.1,
};
if(bigN > 8) //Everything after row 8 is all 0's
{
for(i = 8; i < bigN; i++)
{
table[i][0] = i;
for(j = 1; j < 3;j++)
{
table[i][j] = 0.0; //set to 0.0
}
}
}
int sendandrecvct = (bigN / comm_sz) * 3; //how much to send and
recieve??
MPI_Scatter(table,sendandrecvct,MPI_DOUBLE,subtable,sendandrecvct,MPI_DOUBLE,0,MPI_COMM_WORLD); //scatter the table to subtables
for (k = 0; k < bigN / 2; k++) //K coeffiencet Loop
{
/* Variables used for the computation */
double sumrealeven = 0.0; //sum of real numbers for even
double sumimageven = 0.0; //sum of imaginary numbers for even
double sumrealodd = 0.0; //sum of real numbers for odd
double sumimagodd = 0.0; //sum of imaginary numbers for odd
for(i = 0; i < (bigN/comm_sz)/2; i++) //Sigma loop EVEN and ODD
{
double factoreven , factorodd = 0.0;
int shiftevenonnonzeroP = my_rank * subtable[2*i][0]; //used to shift index numbers for correct results for EVEN.
int shiftoddonnonzeroP = my_rank * subtable[2*i + 1][0]; //used to shift index numbers for correct results for ODD.
/* -------- EVEN PART -------- */
double realeven = subtable[2*i][1]; //Access table for real number at spot 2i
double complex imaginaryeven = subtable[2*i][2]; //Access table for imaginary number at spot 2i
double complex componeeven = (realeven + imaginaryeven * I); //Create the first component from table
if(my_rank == 0) //if proc 0, dont use shiftevenonnonzeroP
{
factoreven = ((2*PI)*((2*i)*k))/bigN; //Calculates the even factor for Cos() and Sin()
// *********Reduces computational time*********
}
else //use shiftevenonnonzeroP
{
factoreven = ((2*PI)*((shiftevenonnonzeroP)*k))/bigN; //Calculates the even factor for Cos() and Sin()
// *********Reduces computational time*********
}
double complex comptwoeven = (cos(factoreven) - (sin(factoreven)*I)); //Create the second component
evenpart[i] = (componeeven * comptwoeven); //store in the evenpart array
/* -------- ODD PART -------- */
double realodd = subtable[2*i + 1][1]; //Access table for real number at spot 2i+1
double complex imaginaryodd = subtable[2*i + 1][2]; //Access table for imaginary number at spot 2i+1
double complex componeodd = (realodd + imaginaryodd * I); //Create the first component from table
if (my_rank == 0)//if proc 0, dont use shiftoddonnonzeroP
{
factorodd = ((2*PI)*((2*i+1)*k))/bigN;//Calculates the odd factor for Cos() and Sin()
// *********Reduces computational time*********
}
else //use shiftoddonnonzeroP
{
factorodd = ((2*PI)*((shiftoddonnonzeroP)*k))/bigN;//Calculates the odd factor for Cos() and Sin()
// *********Reduces computational time*********
}
double complex comptwoodd = (cos(factorodd) - (sin(factorodd)*I));//Create the second component
oddpart[i] = (componeodd * comptwoodd); //store in the oddpart array
}
/*Process ZERO gathers the even and odd part arrays and creates a evenpartmaster and oddpartmaster array*/
MPI_Gather(evenpart,(bigN / comm_sz / 2),MPI_DOUBLE_COMPLEX,evenpartmaster,(bigN / comm_sz / 2), MPI_DOUBLE_COMPLEX,0,MPI_COMM_WORLD);
MPI_Gather(oddpart,(bigN / comm_sz / 2),MPI_DOUBLE_COMPLEX,oddpartmaster,(bigN / comm_sz / 2), MPI_DOUBLE_COMPLEX,0,MPI_COMM_WORLD);
if(my_rank == 0)
{
for(i = 0; i < (bigN / comm_sz / 2) * comm_sz; i++) //loop to sum the EVEN and ODD parts
{
sumrealeven += creal(evenpartmaster[i]); //sums the realpart of the even half
sumimageven += cimag(evenpartmaster[i]); //sums the imaginarypart of the even half
sumrealodd += creal(oddpartmaster[i]); //sums the realpart of the odd half
sumimagodd += cimag(oddpartmaster[i]); //sums the imaginary part of the odd half
}
storeKsumreal[k] = sumrealeven + sumrealodd; //add the calculated reals from even and odd
storeKsumimag[k] = sumimageven + sumimagodd; //add the calculated imaginary from even and odd
storeKsumreal[k + bigN/2] = sumrealeven - sumrealodd; //ABUSE symmetry Xkreal + N/2 = Evenk - OddK
storeKsumimag[k + bigN/2] = sumimageven - sumimagodd; //ABUSE symmetry Xkimag + N/2 = Evenk - OddK
if(k <= 10) //Do the first 10 K's
{
if(k == 0)
{
fprintf(outfile," \n\n TOTAL PROCESSED SAMPLES : %d\n",bigN);
}
fprintf(outfile,"================================\n");
fprintf(outfile,"XR[%d]: %.4f XI[%d]: %.4f \n",k,storeKsumreal[k],k,storeKsumimag[k]);
fprintf(outfile,"================================\n");
}
}
}
if(my_rank == 0)
{
GET_TIME(finish); //stop timer
double timeElapsed = finish-start; //Time for that iteration
avgtime = avgtime + timeElapsed; //AVG the time
fprintf(outfile,"Time Elaspsed on Iteration %d: %f Seconds\n", (h+1),timeElapsed);
}
}
if(my_rank == 0)
{
avgtime = avgtime / howmanytimesavg; //get avg time
fprintf(outfile,"\nAverage Time Elaspsed: %f Seconds", avgtime);
fclose(outfile); //CLOSE file ONLY proc 0 can.
}
MPI_Barrier(MPI_COMM_WORLD); //wait to all proccesses to catch up before finalize
MPI_Finalize(); //End MPI
return 0;
}
错误：
Fatal error in PMPI_Gather: Invalid datatype, error stack:
PMPI_Gather(904): MPI_Gather(sbuf=0x7fffb62799a0, scount=8192,
MPI_DATATYPE_NULL, rbuf=0x7fffb6239980, rcount=8192, MPI_DATATYPE_NULL,
root=0, MPI_COMM_WORLD) failed
PMPI_Gather(815): Datatype for argument sendtype is a null datatype
[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=537490947
:
system msg for write_line failure : Bad file descriptor
您的代码中没有MPI_DATATYPE_NULL，但您只使用了MPI_DOUBLE_COMPLEX。请注意，后一种类型是 Fortran 数据类型，在 C 中使用它严格来说是不正确的。
我的猜测是 MPI_DOUBLE_COMPLEX 导致了问题（类型未定义或未初始化，因为您调用了 MPI_Init() 的 C 版本）。
您显然可以用 Fortran 重写您的代码，或者将您自己的派生数据类型用于 C 双精度复数。
同时，我建议您编写简单的 C 和 Fortran helloworld 程序，使用 MPI_DOUBLE_COMPLEX（例如一个元素的 MPI_Bcast()）来确认问题出在MPI_DOUBLE_COMPLEX 并限制为 C 或不。
我正在尝试运行这个快速傅里叶实现代码。它编译正常，但在 运行 时出现此错误。我不知道错误或它的含义。谁能帮我吗？ 我通过以下方式编译并 运行 程序：
mpicc -o exec test.c
./exec
代码： 这是我在 GITHUB 上找到的代码。它是快速傅里叶算法的并行版本。
#include <stdio.h>
#include <mpi.h> //To use MPI
#include <complex.h> //to use complex numbers
#include <math.h> //for cos() and sin()
#include "timer.h" //to use timer
#define PI 3.14159265
#define bigN 16384 //Problem Size
#define howmanytimesavg 3
int main()
{
int my_rank,comm_sz;
MPI_Init(NULL,NULL); //start MPI
MPI_Comm_size(MPI_COMM_WORLD,&comm_sz); ///how many processes are we
using?
MPI_Comm_rank(MPI_COMM_WORLD,&my_rank); //which process is this?
double start,finish;
double avgtime = 0;
FILE *outfile;
int h;
if(my_rank == 0) //if process 0 open outfile
{
outfile = fopen("ParallelVersionOutput.txt", "w"); //open from current
directory
}
for(h = 0; h < howmanytimesavg; h++) //loop to run multiple times for AVG
time.
{
if(my_rank == 0) //If it's process 0 starts timer
{
start = MPI_Wtime();
}
int i,k,n,j; //Basic loop variables
double complex evenpart[(bigN / comm_sz / 2)]; //array to save the data
for EVENHALF
double complex oddpart[(bigN / comm_sz / 2)]; //array to save the data
for ODDHALF
double complex evenpartmaster[ (bigN / comm_sz / 2) * comm_sz]; //array
to save the data for EVENHALF
double complex oddpartmaster[ (bigN / comm_sz / 2) * comm_sz]; //array
to save the data for ODDHALF
double storeKsumreal[bigN]; //store the K real variable so we can abuse
symmerty
double storeKsumimag[bigN]; //store the K imaginary variable so we can
abuse symmerty
double subtable[(bigN / comm_sz)][3]; //Each process owns a subtable
from the table below
double table[bigN][3] = //TABLE of numbers to use
{
0,3.6,2.6, //n, Real,Imaginary CREATES TABLE
1,2.9,6.3,
2,5.6,4.0,
3,4.8,9.1,
4,3.3,0.4,
5,5.9,4.8,
6,5.0,2.6,
7,4.3,4.1,
};
if(bigN > 8) //Everything after row 8 is all 0's
{
for(i = 8; i < bigN; i++)
{
table[i][0] = i;
for(j = 1; j < 3;j++)
{
table[i][j] = 0.0; //set to 0.0
}
}
}
int sendandrecvct = (bigN / comm_sz) * 3; //how much to send and
recieve??
MPI_Scatter(table,sendandrecvct,MPI_DOUBLE,subtable,sendandrecvct,MPI_DOUBLE,0,MPI_COMM_WORLD); //scatter the table to subtables
for (k = 0; k < bigN / 2; k++) //K coeffiencet Loop
{
/* Variables used for the computation */
double sumrealeven = 0.0; //sum of real numbers for even
double sumimageven = 0.0; //sum of imaginary numbers for even
double sumrealodd = 0.0; //sum of real numbers for odd
double sumimagodd = 0.0; //sum of imaginary numbers for odd
for(i = 0; i < (bigN/comm_sz)/2; i++) //Sigma loop EVEN and ODD
{
double factoreven , factorodd = 0.0;
int shiftevenonnonzeroP = my_rank * subtable[2*i][0]; //used to shift index numbers for correct results for EVEN.
int shiftoddonnonzeroP = my_rank * subtable[2*i + 1][0]; //used to shift index numbers for correct results for ODD.
/* -------- EVEN PART -------- */
double realeven = subtable[2*i][1]; //Access table for real number at spot 2i
double complex imaginaryeven = subtable[2*i][2]; //Access table for imaginary number at spot 2i
double complex componeeven = (realeven + imaginaryeven * I); //Create the first component from table
if(my_rank == 0) //if proc 0, dont use shiftevenonnonzeroP
{
factoreven = ((2*PI)*((2*i)*k))/bigN; //Calculates the even factor for Cos() and Sin()
// *********Reduces computational time*********
}
else //use shiftevenonnonzeroP
{
factoreven = ((2*PI)*((shiftevenonnonzeroP)*k))/bigN; //Calculates the even factor for Cos() and Sin()
// *********Reduces computational time*********
}
double complex comptwoeven = (cos(factoreven) - (sin(factoreven)*I)); //Create the second component
evenpart[i] = (componeeven * comptwoeven); //store in the evenpart array
/* -------- ODD PART -------- */
double realodd = subtable[2*i + 1][1]; //Access table for real number at spot 2i+1
double complex imaginaryodd = subtable[2*i + 1][2]; //Access table for imaginary number at spot 2i+1
double complex componeodd = (realodd + imaginaryodd * I); //Create the first component from table
if (my_rank == 0)//if proc 0, dont use shiftoddonnonzeroP
{
factorodd = ((2*PI)*((2*i+1)*k))/bigN;//Calculates the odd factor for Cos() and Sin()
// *********Reduces computational time*********
}
else //use shiftoddonnonzeroP
{
factorodd = ((2*PI)*((shiftoddonnonzeroP)*k))/bigN;//Calculates the odd factor for Cos() and Sin()
// *********Reduces computational time*********
}
double complex comptwoodd = (cos(factorodd) - (sin(factorodd)*I));//Create the second component
oddpart[i] = (componeodd * comptwoodd); //store in the oddpart array
}
/*Process ZERO gathers the even and odd part arrays and creates a evenpartmaster and oddpartmaster array*/
MPI_Gather(evenpart,(bigN / comm_sz / 2),MPI_DOUBLE_COMPLEX,evenpartmaster,(bigN / comm_sz / 2), MPI_DOUBLE_COMPLEX,0,MPI_COMM_WORLD);
MPI_Gather(oddpart,(bigN / comm_sz / 2),MPI_DOUBLE_COMPLEX,oddpartmaster,(bigN / comm_sz / 2), MPI_DOUBLE_COMPLEX,0,MPI_COMM_WORLD);
if(my_rank == 0)
{
for(i = 0; i < (bigN / comm_sz / 2) * comm_sz; i++) //loop to sum the EVEN and ODD parts
{
sumrealeven += creal(evenpartmaster[i]); //sums the realpart of the even half
sumimageven += cimag(evenpartmaster[i]); //sums the imaginarypart of the even half
sumrealodd += creal(oddpartmaster[i]); //sums the realpart of the odd half
sumimagodd += cimag(oddpartmaster[i]); //sums the imaginary part of the odd half
}
storeKsumreal[k] = sumrealeven + sumrealodd; //add the calculated reals from even and odd
storeKsumimag[k] = sumimageven + sumimagodd; //add the calculated imaginary from even and odd
storeKsumreal[k + bigN/2] = sumrealeven - sumrealodd; //ABUSE symmetry Xkreal + N/2 = Evenk - OddK
storeKsumimag[k + bigN/2] = sumimageven - sumimagodd; //ABUSE symmetry Xkimag + N/2 = Evenk - OddK
if(k <= 10) //Do the first 10 K's
{
if(k == 0)
{
fprintf(outfile," \n\n TOTAL PROCESSED SAMPLES : %d\n",bigN);
}
fprintf(outfile,"================================\n");
fprintf(outfile,"XR[%d]: %.4f XI[%d]: %.4f \n",k,storeKsumreal[k],k,storeKsumimag[k]);
fprintf(outfile,"================================\n");
}
}
}
if(my_rank == 0)
{
GET_TIME(finish); //stop timer
double timeElapsed = finish-start; //Time for that iteration
avgtime = avgtime + timeElapsed; //AVG the time
fprintf(outfile,"Time Elaspsed on Iteration %d: %f Seconds\n", (h+1),timeElapsed);
}
}
if(my_rank == 0)
{
avgtime = avgtime / howmanytimesavg; //get avg time
fprintf(outfile,"\nAverage Time Elaspsed: %f Seconds", avgtime);
fclose(outfile); //CLOSE file ONLY proc 0 can.
}
MPI_Barrier(MPI_COMM_WORLD); //wait to all proccesses to catch up before finalize
MPI_Finalize(); //End MPI
return 0;
}
错误：
Fatal error in PMPI_Gather: Invalid datatype, error stack:
PMPI_Gather(904): MPI_Gather(sbuf=0x7fffb62799a0, scount=8192,
MPI_DATATYPE_NULL, rbuf=0x7fffb6239980, rcount=8192, MPI_DATATYPE_NULL,
root=0, MPI_COMM_WORLD) failed
PMPI_Gather(815): Datatype for argument sendtype is a null datatype
[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=537490947
:
system msg for write_line failure : Bad file descriptor
您的代码中没有MPI_DATATYPE_NULL，但您只使用了MPI_DOUBLE_COMPLEX。请注意，后一种类型是 Fortran 数据类型，在 C 中使用它严格来说是不正确的。
我的猜测是 MPI_DOUBLE_COMPLEX 导致了问题（类型未定义或未初始化，因为您调用了 MPI_Init() 的 C 版本）。
您显然可以用 Fortran 重写您的代码，或者将您自己的派生数据类型用于 C 双精度复数。
同时，我建议您编写简单的 C 和 Fortran helloworld 程序，使用 MPI_DOUBLE_COMPLEX（例如一个元素的 MPI_Bcast()）来确认问题出在MPI_DOUBLE_COMPLEX 并限制为 C 或不。