我正在尝试以非标准的方式编译gpgmg CUDA模拟，因为我没有对我试图运行它的机器的root访问权。
此模拟广泛使用HDF5库（http://www.hdfgroup.org/HDF5/）。当我在没有root访问权限的机器上运行它时，我无法安装HDF5。因此，我下载了文件并将其粘贴在include目录中。我使用以下命令使用NVCC进行编译（是的，我知道这应该是makefile格式）。
nvcc main.cpp CAnnihilationProblem.cpp CCompartment.cpp CDiffusionModel.cpp CFirstOrderReaction.cpp CFisherProblem.cpp CLocalizedAnnihilationProblem.cpp CModel.cpp CReaction.cpp CReactionProblem.cpp CSecondOrderReaction.cpp CSemiInfiniteSlabProblem.cpp CSimpleDiffusionProblem.cpp CSimpleInhomogeneousDiffusionProblem.cpp CSimpleLocalizedFirstOrderReaction.cpp CSimpleLocalizedSecondOrderReaction.cpp CSimpleLocalizedZerothOrderReaction.cpp CZeroOrderReaction.cpp -lgsl -I ../include
这编译很好（如果我只使用-c标志），但当我来链接它时，我得到以下错误：
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/crt1.o: In function `_start':
/usr/src/packages/BUILD/glibc-2.11.1/csu/../sysdeps/x86_64/elf/start.S:109: undefined reference to `main'
/tmp/tmpxft_0000061e_00000000-2_CCompartment.o: In function `gpgmp::CCompartment::saveHdf5(int)':
CCompartment.cpp:(.text+0xbb): undefined reference to `H5Screate_simple'
CCompartment.cpp:(.text+0xc3): undefined reference to `H5open'
CCompartment.cpp:(.text+0xc9): undefined reference to `H5T_NATIVE_INT_g'
CCompartment.cpp:(.text+0x106): undefined reference to `H5Dcreate2'
CCompartment.cpp:(.text+0x13f): undefined reference to `H5open'
CCompartment.cpp:(.text+0x145): undefined reference to `H5T_NATIVE_INT_g'
CCompartment.cpp:(.text+0x164): undefined reference to `H5Dwrite'
CCompartment.cpp:(.text+0x16f): undefined reference to `H5Dclose'
CCompartment.cpp:(.text+0x17a): undefined reference to `H5Sclose'
/tmp/tmpxft_0000061e_00000000-3_CDiffusionModel.o: In function `gpgmp::CDiffusionModel::closeOutputFile(gpgmp::DiffusionModelRuntimeInformation const*)':
CDiffusionModel.cpp:(.text+0x336): undefined reference to `H5Gclose'
CDiffusionModel.cpp:(.text+0x364): undefined reference to `H5Fclose'
/tmp/tmpxft_0000061e_00000000-3_CDiffusionModel.o: In function `gpgmp::CDiffusionModel::prepareOutputFile(gpgmp::DiffusionModelRuntimeInformation*)':
CDiffusionModel.cpp:(.text+0x4bc): undefined reference to `H5check_version'
CDiffusionModel.cpp:(.text+0x4e7): undefined reference to `H5Fopen'
CDiffusionModel.cpp:(.text+0x646): undefined reference to `H5Gcreate2'
CDiffusionModel.cpp:(.text+0x6e8): undefined reference to `H5Gclose'
CDiffusionModel.cpp:(.text+0x719): undefined reference to `H5Fclose'
/tmp/tmpxft_0000061e_00000000-3_CDiffusionModel.o: In function `gpgmp::CDiffusionModel::createOutputFile(gpgmp::DiffusionModelRuntimeInformation*)':
CDiffusionModel.cpp:(.text+0x8f3): undefined reference to `H5check_version'
CDiffusionModel.cpp:(.text+0x923): undefined reference to `H5Fcreate'
CDiffusionModel.cpp:(.text+0x99d): undefined reference to `H5Gcreate2'
CDiffusionModel.cpp:(.text+0x9bb): undefined reference to `H5Screate_simple'
CDiffusionModel.cpp:(.text+0x9c3): undefined reference to `H5open'
CDiffusionModel.cpp:(.text+0x9c9): undefined reference to `H5T_NATIVE_INT_g'
CDiffusionModel.cpp:(.text+0x9ec): undefined reference to `H5Dcreate2'
CDiffusionModel.cpp:(.text+0xa06): undefined reference to `H5open'
CDiffusionModel.cpp:(.text+0xa0c): undefined reference to `H5T_NATIVE_INT_g'
CDiffusionModel.cpp:(.text+0xa2b): undefined reference to `H5Dwrite'
CDiffusionModel.cpp:(.text+0xa36): undefined reference to `H5Dclose'
CDiffusionModel.cpp:(.text+0xa41): undefined reference to `H5Sclose'
CDiffusionModel.cpp:(.text+0xad0): undefined reference to `H5open'
CDiffusionModel.cpp:(.text+0xad6): undefined reference to `H5T_C_S1_g'
CDiffusionModel.cpp:(.text+0xadb): undefined reference to `H5Tcopy'
CDiffusionModel.cpp:(.text+0xaed): undefined reference to `H5Tset_size'
CDiffusionModel.cpp:(.text+0xb03): undefined reference to `H5Screate_simple'
CDiffusionModel.cpp:(.text+0xb2c): undefined reference to `H5Dcreate2'
CDiffusionModel.cpp:(.text+0xb51): undefined reference to `H5Dwrite'
CDiffusionModel.cpp:(.text+0xb5c): undefined reference to `H5Dclose'
CDiffusionModel.cpp:(.text+0xb67): undefined reference to `H5Sclose'
CDiffusionModel.cpp:(.text+0xb8e): undefined reference to `H5Screate_simple'
CDiffusionModel.cpp:(.text+0xb96): undefined reference to `H5open'
CDiffusionModel.cpp:(.text+0xb9c): undefined reference to `H5T_NATIVE_INT_g'
CDiffusionModel.cpp:(.text+0xbbf): undefined reference to `H5Dcreate2'
CDiffusionModel.cpp:(.text+0xbd9): undefined reference to `H5open'
CDiffusionModel.cpp:(.text+0xbdf): undefined reference to `H5T_NATIVE_INT_g'
CDiffusionModel.cpp:(.text+0xbfe): undefined reference to `H5Dwrite'
CDiffusionModel.cpp:(.text+0xc09): undefined reference to `H5Dclose'
CDiffusionModel.cpp:(.text+0xc14): undefined reference to `H5Sclose'
CDiffusionModel.cpp:(.text+0xc34): undefined reference to `H5Gcreate2'
CDiffusionModel.cpp:(.text+0xcb4): undefined reference to `H5Gclose'
CDiffusionModel.cpp:(.text+0xcbf): undefined reference to `H5Gclose'
/tmp/tmpxft_0000061e_00000000-3_CDiffusionModel.o: In function `gpgmp::CDiffusionModel::openOutputFile(gpgmp::DiffusionModelRuntimeInformation*)':
CDiffusionModel.cpp:(.text+0xe1d): undefined reference to `H5check_version'
CDiffusionModel.cpp:(.text+0xe48): undefined reference to `H5Fopen'
CDiffusionModel.cpp:(.text+0xf9c): undefined reference to `H5Gopen2'
/tmp/tmpxft_0000061e_00000000-3_CDiffusionModel.o: In function `gpgmp::CDiffusionModel::writeAllSpecies(float, gpgmp::DiffusionModelRuntimeInformation*)':
CDiffusionModel.cpp:(.text+0x141b): undefined reference to `H5Gcreate2'
CDiffusionModel.cpp:(.text+0x147f): undefined reference to `H5Screate_simple'
CDiffusionModel.cpp:(.text+0x1487): undefined reference to `H5open'
CDiffusionModel.cpp:(.text+0x148d): undefined reference to `H5T_NATIVE_FLOAT_g'
CDiffusionModel.cpp:(.text+0x14b0): undefined reference to `H5Dcreate2'
CDiffusionModel.cpp:(.text+0x14b8): undefined reference to `H5open'
CDiffusionModel.cpp:(.text+0x14be): undefined reference to `H5T_NATIVE_FLOAT_g'
CDiffusionModel.cpp:(.text+0x14e0): undefined reference to `H5Dwrite'
CDiffusionModel.cpp:(.text+0x14eb): undefined reference to `H5Dclose'
CDiffusionModel.cpp:(.text+0x14f6): undefined reference to `H5Sclose'
CDiffusionModel.cpp:(.text+0x15c6): undefined reference to `H5Screate_simple'
CDiffusionModel.cpp:(.text+0x15ce): undefined reference to `H5open'
CDiffusionModel.cpp:(.text+0x15d4): undefined reference to `H5T_NATIVE_INT_g'
CDiffusionModel.cpp:(.text+0x161e): undefined reference to `H5Dcreate2'
CDiffusionModel.cpp:(.text+0x165e): undefined reference to `H5open'
CDiffusionModel.cpp:(.text+0x1664): undefined reference to `H5T_NATIVE_INT_g'
CDiffusionModel.cpp:(.text+0x1683): undefined reference to `H5Dwrite'
CDiffusionModel.cpp:(.text+0x168e): undefined reference to `H5Dclose'
CDiffusionModel.cpp:(.text+0x1699): undefined reference to `H5Sclose'
CDiffusionModel.cpp:(.text+0x16bb): undefined reference to `H5Gclose'
/tmp/tmpxft_0000061e_00000000-3_CDiffusionModel.o: In function `gpgmp::CDiffusionModel::runSomeGmps(void*)':
CDiffusionModel.cpp:(.text+0x17ff): undefined reference to `chooseDevice(int)'
CDiffusionModel.cpp:(.text+0x1883): undefined reference to `gpgmp::CDiffusionModel::cudaRunGMPInhomogeneous(gpgmp::DiffusionModelRuntimeInformation*)'
CDiffusionModel.cpp:(.text+0x1892): undefined reference to `gpgmp::CDiffusionModel::cudaRunGMP(gpgmp::DiffusionModelRuntimeInformation*)'
/tmp/tmpxft_0000061e_00000000-3_CDiffusionModel.o: In function `gpgmp::CDiffusionModel::runMultipleGmps(int, int, float, float, float, int, bool, void*)':
CDiffusionModel.cpp:(.text+0x2b4d): undefined reference to `queryCudaDevices()'
/tmp/tmpxft_0000061e_00000000-7_CModel.o: In function `gpgmp::CModel::gillespie(int, bool)':
CModel.cpp:(.text+0x8d9): undefined reference to `gpgmp::cudaRunGillespie(float*, int*, float*, float*, gpgmp::RateLaw*, int, int, int)'
collect2: ld returned 1 exit status
我的第一个想法是main()没有被定义，但确实如此。这是main.cpp：
#include "CModel.h"
#include "CDiffusionModel.h"
#include "CAnnihilationProblem.h"
#include "CSemiInfiniteSlabProblem.h"
#include "CSimpleDiffusionProblem.h"
#include "CSimpleInhomogeneousDiffusionProblem.h"
#include "CLocalizedAnnihilationProblem.h"
#include "CFisherProblem.h"
#include "CReactionProblem.h"
#include "definitions.h"
#include "CSecondOrderReaction.h"
#include <getopt.h>
#include <cstdio>
#include <iostream>
using namespace std;
int chooseCudaDevice(int device);
int main(int argc, char **argv) {
// parameters
int dx=32, dy=32;
int numRuns=10;
int numSteps=500000;
float time=100.;
REAL length=40.;
//opterr = 0;
int c;
int numCudaDevices=-1;
int problem=0;
float p0 = 0.1;
float dt = 0.1;
gpgmp::OutputFormat outputFormat = gpgmp::OUTPUT_HDF5;
while ((c = getopt (argc, argv, "x:y:t:l:n:r:d:p:w:o:f:")) != -1)
switch (c)
{
case 'x':
dx = atoi(optarg);
break;
case 'y':
dy = atoi(optarg);
break;
case 't':
time = atof(optarg);
break;
case 'l':
length = atof(optarg);
break;
case 'n':
numSteps = atoi(optarg);
break;
case 'r':
numRuns = atoi(optarg);
break;
case 'd':
// number of devices to run on
numCudaDevices = atoi(optarg);
break;
case 'p':
problem = atoi(optarg);
break;
case 'o':
dt = atof(optarg);
break;
case 'w':
p0 = atof(optarg);
break;
case 'f':
switch(atoi(optarg)) {
case 0:
cout <<"Setting output format to ASCII.\n";
outputFormat = gpgmp::OUTPUT_ASCII;
break;
case 1:
cout <<"Setting output format to HDF5.\n";
outputFormat = gpgmp::OUTPUT_HDF5;
break;
}
break;
case '?':
if (optopt == 'x' || optopt =='y' || optopt == 't'
|| optopt =='l' || optopt == 'n' || optopt=='r' || optopt=='d'
|| optopt=='p' || optopt == 'w')
fprintf (stderr, "Option -%c requires an argument.\n", optopt);
else if (isprint (optopt))
fprintf (stderr, "Unknown option `-%c'.\n", optopt);
else
fprintf (stderr,
"Unknown option character `\\x%x'.\n",
optopt);
return 1;
default:
abort ();
}
int index=optind;
cout <<"Welcome to gmp.\n";
cout <<"System dimensions: length="<<length
<<", dx="<<dx<<", dy="<<dy<<"\n";
cout <<"Runtime configuration: time="<<time
<<", number of Runs="<<numRuns
<<", number of Steps="<<numSteps
<<", output dt="<<dt
<<", problem nr="<<problem
<<"\n";
if (problem == 0) {
// A plus B reaction model
float diffusionConstant;
float k1;
float k2;
float k3;
float k4;
if (index == argc-5) {
diffusionConstant=atof(argv[index++]);
k1=atof(argv[index++]);
k2=atof(argv[index++]);
k3=atof(argv[index++]);
k4=atof(argv[index++]);
} else if (index==argc) {
cout <<"No parameters given, using default.\n";
length=100.;
dx=128;
dy=128;
p0=0.1;
time=500.;
k1=1e-3;
k2=1e-2;
k3=1.2;
k4=1.;
diffusionConstant=0.;
} else {
cout <<"Mismatching parameters. Usage:\n";
cout <<"gpgmp -p 3 [diffusionConstant k1 k2 k3 k4].\n";
exit(1);
}
cout <<"Setting up A plus B reaction problem with diffusion Constant :"
<<diffusionConstant<<"\n";
cout <<"k1 = "<<k1<<", k2 = "<<k2<<", k3 = "<<k3<<", k4 = "<<k4<<"\n";
gpgmp::CReactionProblem reaction(length, dx, dy, diffusionConstant, k1, k2, k3, k4);
reaction.setOutputFormat(outputFormat);
reaction.runMultipleGmps(numRuns, numSteps, time, p0, dt);
} else if (problem == 1) {
// FISHER PROBLEM
float baseConcentration = atof(argv[index++]);
cout <<"Setting up Fisher Problem with concentration "<<baseConcentration<<".\n";
gpgmp::CFisherProblem fisher(length, dx, dy, baseConcentration);
fisher.setOutputFormat(gpgmp::OUTPUT_HDF5);
fisher.runMultipleGmps(numRuns, numSteps, time, p0, dt);
} else if (problem == 2) {
// SIMPLE DIFFUSION
float diffusionConstant;
int numMolecules;
if (index == argc-2) {
diffusionConstant=atof(argv[index++]);
numMolecules = atoi(argv[index++]);
} else if (index==argc) {
cout <<"No parameters given, using default.\n";
length=100.;
dx=128;
dy=128;
p0=0.1;
dt = 5.;
time=20.;
diffusionConstant=1.;
numMolecules = 1e5;
} else {
cout <<"Mismatching parameters. Usage:\n";
cout <<"gpgmp -p 2 [diffusionConstant numMolecules].\n";
exit(1);
}
cout <<"Setting up simple diffusion problem with diffusion Constant :"<<diffusionConstant
<<", nMol:"<<numMolecules<<" \n";
gpgmp::CSimpleDiffusionProblem diffusion(
length, dx, dy, diffusionConstant, numMolecules);
diffusion.setOutputFormat(gpgmp::OUTPUT_HDF5);
diffusion.runMultipleGmps(numRuns, numSteps, time, p0, dt,numCudaDevices);
} else if (problem ==3) {
// LOCALIZED A+B ANNIHILATION
cout <<"Setting up localized A plus B reaction problem.\n";
float diffusionConstant;
float k1, k2, k3, k4;
float xminA, xmaxA,xminB, xmaxB;
if (index == argc-9) {
diffusionConstant=atof(argv[index++]);
k1=atof(argv[index++]);
k2=atof(argv[index++]);
k3=atof(argv[index++]);
k4=atof(argv[index++]);
xminA=atof(argv[index++]);
xmaxA=atof(argv[index++]);
xminB=atof(argv[index++]);
xmaxB=atof(argv[index++]);
} else if (index==argc) {
cout <<"No parameters given, using default.\n";
length=1000.;
dx=32;
dy=32;
p0=0.1;
time=1800.;
k1=9.4096e+09;
k2=9.4096e+10;
k3=1.27529e-13;
k4=1.06274e-13;
diffusionConstant=100.;
xminA = 0.;
xmaxA = 900.;
xminB = 400.;
xmaxB = 1000.;
} else {
cout <<"Mismatching parameters. Usage:\n";
cout <<"gpgmp -p 3 [diffusionConstant k1 k2 k3 k4 xminA xmaxA xminB xmaxB].\n";
exit(1);
}
cout <<"Parameters : diffusion Constant :"<<diffusionConstant<<"\n";
cout <<"k1 = "<<k1<<", k2 = "<<k2<<", k3 = "<<k3<<", k4 = "<<k4<<"\n";
cout <<"xminA = "<<xminA<<", xmaxA = "<<xmaxA<<", xminB = "<<xminB<<", xmaxB = "<<xmaxB<<"\n";
gpgmp::CLocalizedAnnihilationProblem problem(length, dx, dy,
diffusionConstant, k1, k2, k3, k4,
xminA, xmaxA, xminB, xmaxB);
problem.runMultipleGmps(numRuns, numSteps, time, p0, dt);
} else if (problem == 4) {
// SEMI-INFINITE SLAB problem
cout <<"Setting up semi-infinite slab problem.\n";
float diffusionConstant;
float sourceNumber;
if (index == argc-2) {
diffusionConstant=atof(argv[index++]);
sourceNumber=atof(argv[index++]);
} else if (index==argc) {
cout <<"No parameters given, using default.\n";
length=40.;
dx=64;
dy=64;
p0=0.1;
time=1000;
diffusionConstant=1.;
sourceNumber = 10.;
dt=500.;
} else {
cout <<"Mismatching parameters. Usage:\n";
cout <<"gpgmp -p 4 [diffusionConstant sourceNumber].\n";
exit(1);
}
cout <<"Setting up semi-infinite slab problem.\n";
cout <<"Source number is:"<<sourceNumber<<", diffusion Constant:"
<<diffusionConstant<<"\n";
gpgmp::CSemiInfiniteSlabProblem
slabModel(length, dx, dy, sourceNumber, diffusionConstant);
slabModel.setOutputFormat(gpgmp::OUTPUT_HDF5);
slabModel.runMultipleGmps(numRuns, numSteps, time, p0, dt);
} else if (problem == 5) {
// Sets up the A+B annihilation model
REAL length = 12.8; // In micrometer
REAL nx = 64; // Number of cells in each direction
gpgmp::CDiffusionModel testModel(length, nx, nx);
// add species to model
REAL diffusivity = 1; // In micrometer^2 s^-1
testModel.addDiffusionSpecies("A", diffusivity);
testModel.addDiffusionSpecies("B", diffusivity);
testModel.addDiffusionSpecies("C", diffusivity);
// create "source" and "world" compartments
gpgmp::CCompartment comp1("Source", 32, 32, 32, 32);
gpgmp::CCompartment comp2("World",0, 0, 63, 63);
// add species to compartment
comp1.setInitialAmount("A", 1000, gpgmp::DIST_HOMOGENEOUS);
comp2.setInitialAmount("B", 1000, gpgmp::DIST_RANDOM);
// and add it to the main model
testModel.addCompartment(0, comp1);
testModel.addCompartment(1, comp2);
// add the annihilation reaction
// A+B -> C
REAL reactionRate = 1e8; // Reaction rate in M^-1 s^-1
// set the reaction products
std::map<std::string, int> aplusbAnnihilationMap;
aplusbAnnihilationMap["C"]=1;
// and create the reaction
gpgmp::CSecondOrderReaction *aplusbAnnihilation =
new gpgmp::CSecondOrderReaction("A plus B annihilation",
testModel.getSecondOrderReactionRate(reactionRate),
"A", "B", aplusbAnnihilationMap);
testModel.addReaction(aplusbAnnihilation);
// set output format
testModel.setOutputFormat(gpgmp::OUTPUT_HDF5);
// run the GMP to test the output
int nRuns = 100; // Number of runs
int nSteps = 10000; // Max number of steps
REAL simTime = 5.; // Max simulation time
REAL p = 0.1; // Probability for a particle to stay
REAL dumpTime = 1.; // Interval of output dumps
testModel.runMultipleGmps(nRuns, nSteps, simTime, p, dumpTime);
} else if (problem==6) {
// 2D A+B annihilation problem
std::cout <<"Setting up 2D annihilation problem.";
// default parameters
REAL diffusionConstant = 1.;
REAL rate;
int numMolecules;
// check if more parameters are given - if not take defaults
if (index == argc-3) {
diffusionConstant=atof(argv[index++]);
rate=atof(argv[index++]);
numMolecules = atoi(argv[index++]);
} else if (index == argc) {
// use defaults
cout <<"No parameters given ... using defaults.\n";
length=12.8;
dx=64;
dy=64;
p0=0.1;
time=4.;
rate = 1e8;
numMolecules = 100000.;
} else {
cout <<"Mismatching parameters. Usage:\n";
cout <<"gpgmp -p 6 diffusionConstant rate numMolecules.\n";
exit(1);
}
std::cout <<"Annihilation rate is:"<<rate<<", diffusion Constant:"
<<diffusionConstant<<", number of Molecules:"
<<numMolecules<<".\n";
gpgmp::CAnnihilationProblem model(length, dx, dy, numMolecules,
diffusionConstant, rate);
model.setOutputFormat(outputFormat);
model.runMultipleGmps(numRuns, numSteps, time, p0, dt,numCudaDevices);
} else if (problem == 7) {
// SIMPLE INHOMOGENEOUS DIFFUSION
float diffusionConstant=atof(argv[index++]);
int numMolecules = atoi(argv[index++]);
int testModel = atoi(argv[index++]);
gpgmp::InhomogeneousDiffusionParameters kernelParams;
// set dimensionality
kernelParams.dimensionality = 1;
cout <<"Setting up simple inhomogeneous diffusion problem with diffusion Constant :"
<<diffusionConstant <<", nMol:"<<numMolecules<<".\n";
cout <<"Test model is ";
REAL u0, a;
gpgmp::CSimpleInhomogeneousDiffusionProblem *diffusion;
switch (testModel) {
case 0:
cout <<"constant diffusivity.\n";
kernelParams.diffusionType =
gpgmp::InhomogeneousDiffusionParameters::DT_HOMOGENEOUS;
diffusion = new gpgmp::CSimpleInhomogeneousDiffusionProblem(
length, dx, dy, diffusionConstant, numMolecules, true);
break;
case 1:
u0 = atof(argv[index++]);
cout <<"population pressure model with u0="<<u0<<".\n";
kernelParams.diffusionType =
gpgmp::InhomogeneousDiffusionParameters::DT_LOCAL_AVERAGE;
kernelParams.testModelType =
gpgmp::InhomogeneousDiffusionParameters::TM_POPULATION_PRESSURE;
kernelParams.u0 = u0;
diffusion = new gpgmp::CSimpleInhomogeneousDiffusionProblem(
length, dx, dy, diffusionConstant, numMolecules, false);
break;
case 2:
a = atof(argv[index++]);
cout <<"contact inhibition model with A="<<a<<".\n";
kernelParams.diffusionType =
gpgmp::InhomogeneousDiffusionParameters::DT_LOCAL_AVERAGE;
kernelParams.testModelType =
gpgmp::InhomogeneousDiffusionParameters::TM_CONTACT_INHIBITION;
kernelParams.a = a;
diffusion = new gpgmp::CSimpleInhomogeneousDiffusionProblem(
length, dx, dy, diffusionConstant, numMolecules, false);
break;
}
diffusion->runMultipleGmps(numRuns, numSteps, time, p0, dt,numCudaDevices,
true, (void *) &kernelParams);
} else if (problem == 8) {
// Slit Problem
REAL length = 1200.;
gpgmp::CDiffusionModel testModel(length, dx, dy);
// create new Compartment
gpgmp::CCompartment comp1("Explant", dx/2-1, dy/2-1, dx/2, dy/2);
// add species to compartment
comp1.setInitialAmount("Cells", 20398, gpgmp::DIST_HOMOGENEOUS);
// and add it to the main model
testModel.addCompartment(0, comp1);
// add species
testModel.addDiffusionSpecies("Cells", 0.56);
// create the kernel parameters structure
gpgmp::InhomogeneousDiffusionParameters kernelParams;
kernelParams.dimensionality = 2;
kernelParams.testModelType =
gpgmp::InhomogeneousDiffusionParameters::TM_SLIT;
// slit parameters
kernelParams.lambda = 0.01;
kernelParams.beta = 20;
kernelParams.length = length;
REAL subVolume = length/dx*length/dx;
kernelParams.a = 0.02*subVolume;
kernelParams.ta = 24.*3600.;
kernelParams.xi = 1e4/3600.;
// set diffusion type
int diffType = atoi(argv[index++]);
switch(diffType) {
case 0:
kernelParams.diffusionType =
gpgmp::InhomogeneousDiffusionParameters::DT_STRICTLY_LOCAL;
break;
case 1:
kernelParams.diffusionType =
gpgmp::InhomogeneousDiffusionParameters::DT_LOCAL_AVERAGE;
break;
case 2:
kernelParams.diffusionType =
gpgmp::InhomogeneousDiffusionParameters::DT_NEIGHBOUR_BASED;
break;
case 3:
kernelParams.diffusionType =
gpgmp::InhomogeneousDiffusionParameters::DT_GRADIENT_BASED;
break;
}
// run the GMP to test the output
testModel.runMultipleGmps(numRuns, numSteps, time, p0, dt, numCudaDevices,
true, (void *) &kernelParams);
}
}
由于这是经过同行评审的代码，我假设错误与我链接它的方式有关....
如何才能正确链接？
答案 0 :(得分：1)
您必须显式链接代码中的库依赖项。这里的错误是由于没有链接合适的HDF5库而导致不满意的依赖性。如果您在相对于工作目录的路径../include中安装了缺少的库，那么就像这样：
nvcc -I ../include main.cpp CAnnihilationProblem.cpp CCompartment.cpp CDiffusionModel.cpp \
CFirstOrderReaction.cpp CFisherProblem.cpp CLocalizedAnnihilationProblem.cpp \
CModel.cpp CReaction.cpp CReactionProblem.cpp CSecondOrderReaction.cpp
CSemiInfiniteSlabProblem.cpp CSimpleDiffusionProblem.cpp \
CSimpleInhomogeneousDiffusionProblem.cpp \
CSimpleLocalizedFirstOrderReaction.cpp CSimpleLocalizedSecondOrderReaction.cpp \
CSimpleLocalizedZerothOrderReaction.cpp CZeroOrderReaction.cpp \
-L../include -lgsl -lhdf5
应该允许代码正确链接。
[此答案汇总自评论作为社区维基条目，以便将问题从未答复的列表中删除]。