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#include <string>
#include <unistd.h>
#include "base/CommandLineParser.h"
#include "base/FileParser.h"
class JobControl
{
public:
JobControl(int n, bool bLSF) {
m_n = n;
m_run = 0;
m_bLSF = bLSF;
}
void Add(const string & cmmd, const string & out, const string & log, const string &err) {
m_cmmd.push_back(cmmd);
m_out.push_back(out);
m_log.push_back(log);
m_err.push_back(err);
m_sub.push_back(0);
}
int Remaining() {
return m_cmmd.isize();
}
void Submit() {
int i;
// Check if they are done...
for (i=0; i<m_sub.isize(); i++) {
if (m_sub[i] == 0)
continue;
FILE * p = fopen(m_err[i].c_str(), "r");
if (p == NULL)
continue;
fclose(p);
FlatFileParser parser;
parser.Open(m_err[i]);
bool bDone = false;
while (parser.ParseLine()) {
if (parser.Line() == "Done") {
bDone = true;
}
}
if (bDone) {
Remove(i);
cout << "JC: Done, removing: " << i << endl;
m_run--;
i--;
}
}
//cout << "JC: Running: " << m_run << endl;
//cout << "JC: Possibly submitting " << m_n - m_run << " new jobs." << endl;
if (m_run == m_n)
return;
for (i=0; i<m_sub.isize(); i++) {
if (m_sub[i] == 0) {
m_sub[i] = 1;
m_run++;
if (!m_bLSF) {
string theCmmd = m_cmmd[i];
theCmmd += " >& ";
theCmmd += m_log[i];
theCmmd += " &";
system(theCmmd.c_str());
cout << "JC: Start job: " << theCmmd << endl;
} else {
string theCmmd = "bsub -o ";
theCmmd += m_log[i];
theCmmd += " ";
theCmmd += m_cmmd[i];
cout << "JC: Start job on farm: " << theCmmd << endl;
system(theCmmd.c_str());
}
if (m_run >= m_n)
break;
}
}
}
void ClearFiles() {
for (int i=0; i<m_err.isize(); i++) {
//if (m_sub[i] == 0)
//continue;
FILE * p = fopen(m_err[i].c_str(), "r");
if (p == NULL)
continue;
fclose(p);
string rm = "rm " + m_err[i];
cout << "Running: " << rm << endl;
cout << rm << endl;
system(rm.c_str());
}
}
void Remove(int i) {
int n = m_cmmd.isize()-1;
if (n < 0)
return;
m_cmmd[i] = m_cmmd[n];
m_out[i] = m_out[n];
m_sub[i] = m_sub[n];
m_log[i] = m_log[n];
m_err[i] = m_err[n];
m_cmmd.resize(n);
m_sub.resize(n);
m_out.resize(n);
m_log.resize(n);
m_err.resize(n);
}
private:
bool m_bLSF;
int m_n;
int m_run;
svec<int> m_sub;
svec<string> m_cmmd;
svec<string> m_out;
svec<string> m_log;
svec<string> m_err;
};
int main( int argc, char** argv )
{
commandArg<string> fileCmmd("-i","input file");
commandArg<int> nCmmd("-n","number of CPUs", 1);
commandArg<bool> lsfCmmd("-lsf","run on LSF or not",false);
commandLineParser P(argc,argv);
P.SetDescription("Parallel execution of butterfly on a local server or on the LSF farm.");
P.registerArg(fileCmmd);
P.registerArg(nCmmd);
P.registerArg(lsfCmmd);
P.parse();
string fileName = P.GetStringValueFor(fileCmmd);
int nCPUs = P.GetIntValueFor(nCmmd);
bool bLSF = P.GetBoolValueFor(lsfCmmd);
//comment. ???
FlatFileParser parser;
parser.Open(fileName);
JobControl jc(nCPUs, bLSF);
jc.ClearFiles();
cout << "Reading command list..." << endl;
//!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
//parser.ParseLine();
while (parser.ParseLine()) {
if (parser.GetItemCount() == 0)
continue;
string out = parser.AsString(parser.GetItemCount()-1);
string log = out;
string err = out;
out += "_allProbPaths.fasta";
log += ".log";
err += ".err";
jc.Add(parser.Line(), out, log, err);
}
jc.ClearFiles();
//return 0;
do {
//cout << "Submitting a batch." << endl;
jc.Submit();
//usleep(100000);
sleep(1);
} while (jc.Remaining() > 0);
return 0;
}
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