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PODynamic Allocation of huge 3D arrays
 

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    <p>I am working on a project where I need to create a 3D array, some 2D and 1D arrays. The 3D array represents discrete co-ordinates in space and I need lots of points for my problem. The array size will be around 2000*2000*2000. I need store 'double' values in these arrays. Can anyone suggest an efficient scheme to implement this in C?</p> <p>Thanks in advance </p> <pre><code>/*********************************************************** * Copyright Univ. of Texas M.D. Anderson Cancer Center * 1992. * * Some routines modified from Numerical Recipes in C, * including error report, array or matrix declaration * and releasing. ****/ #include &lt;stdlib.h&gt; #include &lt;stdio.h&gt; #include &lt;math.h&gt; #include &lt;malloc.h&gt; /*********************************************************** * Report error message to stderr, then exit the program * with signal 1. ****/ void nrerror(char error_text[]) { fprintf(stderr,"%s\n",error_text); fprintf(stderr,"...now exiting to system...\n"); exit(1); } /*********************************************************** * Allocate an array with index from nl to nh inclusive. * * Original matrix and vector from Numerical Recipes in C * don't initialize the elements to zero. This will * be accomplished by the following functions. ****/ double *AllocVector(short nl, short nh) { double *v; short i; v=(double *)malloc((unsigned) (nh-nl+1)*sizeof(double)); if (!v) nrerror("allocation failure in vector()"); v -= nl; for(i=nl;i&lt;=nh;i++) v[i] = 0.0; /* init. */ return v; } /*********************************************************** * Allocate a matrix with row index from nrl to nrh * inclusive, and column index from ncl to nch * inclusive. ****/ double **AllocMatrix(short nrl,short nrh, short ncl,short nch) { short i,j; double **m; m=(double **) malloc((unsigned) (nrh-nrl+1) *sizeof(double*)); if (!m) nrerror("allocation failure 1 in matrix()"); m -= nrl; for(i=nrl;i&lt;=nrh;i++) { m[i]=(double *) malloc((unsigned) (nch-ncl+1) *sizeof(double)); if (!m[i]) nrerror("allocation failure 2 in matrix()"); m[i] -= ncl; } for(i=nrl;i&lt;=nrh;i++) for(j=ncl;j&lt;=nch;j++) m[i][j] = 0.0; return m; } /*********************************************************** * Allocate a 3D array with x index from nxl to nxh * inclusive, y index from nyl to nyh and z index from nzl to nzh * inclusive. ****/ double ***Alloc3D(short nxl,short nxh, short nyl,short nyh, short nzl, short nzh) { double ***t; short i,j,k; t=(double ***) malloc((unsigned) (nxh-nxl+1)*sizeof(double **)); if (!t) nrerror("allocation failure 1 in matrix()"); t -= nxl; for(i=nxl;i&lt;=nxh;i++) { t[i]=(double **) malloc((unsigned) (nyh-nyl+1)*sizeof(double *)); if (!t[i]) nrerror("allocation failure 2 in matrix()"); t[i] -= nyl; for(j=nyl;j&lt;=nyh;j++) { t[i][j]=(double *) malloc((unsigned) (nzh-nzl+1)*sizeof(double)); if (!t[i][j]) nrerror("allocation failure 3 in matrix()"); t[i][j] -= nzl;} } for(i=nxl;i&lt;=nxh;i++) for(j=nyl;j&lt;=nyh;j++) for(k=nzl; k&lt;=nzh;k++) t[i][j][k] = 0.0; return t; } /*********************************************************** *Index to 3D array. ****/ long index(int x, int y, int z, int Size) { return (Size*Size*x + Size*y + z); } /*********************************************************** * Release the memory. ****/ void FreeVector(double *v,short nl,short nh) { free((char*) (v+nl)); } /*********************************************************** * Release the memory. ****/ void FreeMatrix(double **m,short nrl,short nrh, short ncl,short nch) { short i; for(i=nrh;i&gt;=nrl;i--) free((char*) (m[i]+ncl)); free((char*) (m+nrl)); } /*********************************************************** * Release the memory. ****/ void Free3D(double ***t,short nxl,short nxh, short nyl,short nyh, short nzl, short nzh) { short i,j; for(i=nxh;i&gt;=nxl;i--) {for(j=nyl;j&gt;=nyl;j--) free((char*) (t[i][j]+nzl)); free((char*) (t[i]+nyl)); } free((char*) (t+nxl)); } *********************************************************************************** void InitOutputData(InputStruct In_Parm, OutStruct * Out_Ptr) { short nz = In_Parm.nz; short nr = In_Parm.nr; short na = In_Parm.na; short nl = In_Parm.num_layers; short size = nr/2*nr/2*nz; /* remember to use nl+2 because of 2 for ambient. */ if(nz&lt;=0 || nr&lt;=0 || na&lt;=0 || nl&lt;=0) nrerror("Wrong grid parameters.\n"); /* Init pure numbers. */ Out_Ptr-&gt;Rsp = 0.0; Out_Ptr-&gt;Rd = 0.0; Out_Ptr-&gt;A = 0.0; Out_Ptr-&gt;Tt = 0.0; /* Allocate the arrays and the matrices. */ //Out_Ptr-&gt;Rd_ra = AllocMatrix(0,nr-1,0,na-1); //Out_Ptr-&gt;Rd_r = AllocVector(0,nr-1); //Out_Ptr-&gt;Rd_a = AllocVector(0,na-1); Out_Ptr-&gt;A_xyz1 = AllocVector(0,size-1); Out_Ptr-&gt;A_xyz2 = AllocVector(0,size-1); Out_Ptr-&gt;A_xyz3 = AllocVector(0,size-1); Out_Ptr-&gt;A_xyz4 = AllocVector(0,size-1); Out_Ptr-&gt;A_xz = AllocMatrix(0,nr-1,0,nz-1); Out_Ptr-&gt;A_z = AllocVector(0,nz-1); Out_Ptr-&gt;A_l = AllocVector(0,nl+1); Out_Ptr-&gt;Tt_ra = AllocMatrix(0,nr-1,0,na-1); Out_Ptr-&gt;Tt_r = AllocVector(0,nr-1); Out_Ptr-&gt;Tt_a = AllocVector(0,na-1); } </code></pre> <p>Above is the code for allocating the arrays and the function to call them. The call which fails is 'Out_Ptr->A_xyz1 = AllocVector(0,size-1);' when size is more than approx. 7000.</p>
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    1. COIs it going to be a sparse array?
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    2. CODo the coordinates represent a regular grid? i.e. Must you store the values or can they be calculated when needed from a grid-spacing within an extents rectangle?
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    3. CODo you need to access the array mostly in sequence or random access? You could memory-map parts of a big file to store the values. Can't do random access then though.
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